3-183722184-A-AG

Variant names:

• chr3-183722184-A-AG
• rs3841649
• NM_018023.5:c.537+48_537+49insG

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_018023.5(YEATS2):​c.537+48_537+49insG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 1,585,528 control chromosomes in the GnomAD database, including 183,882 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.45 (15874 hom., cov: 0)
  • Exomes 𝑓: 0.48 (168008 hom.)
• Consequence: YEATS2 NM_018023.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.168
• Publications: 6 publications found

Genes affected

YEATS2 (HGNC:25489): (YEATS domain containing 2) Summary: The protein encoded by this gene is a scaffolding subunit of the ATAC complex, which is a complex with acetyltransferase activity on histones H3 and H4. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2017]

YEATS2 Gene-Disease associations (from GenCC):

• benign adult familial myoclonic epilepsy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 3-183722184-A-AG is Benign according to our data. Variant chr3-183722184-A-AG is described in ClinVar as Benign. ClinVar VariationId is 1684243.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018023.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YEATS2	NM_018023.5	MANE Select	c.537+48_537+49insG		intron	N/A	NP_060493.3
	YEATS2	NM_001351370.2		c.537+48_537+49insG		intron	N/A	NP_001338299.1
	YEATS2	NM_001351369.2		c.537+48_537+49insG		intron	N/A	NP_001338298.1	Q9ULM3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YEATS2	ENST00000305135.10	TSL:1 MANE Select	c.537+48_537+49insG		intron	N/A	ENSP00000306983.5	Q9ULM3
	YEATS2	ENST00000884732.1		c.537+48_537+49insG		intron	N/A	ENSP00000554791.1
	YEATS2	ENST00000884736.1		c.537+48_537+49insG		intron	N/A	ENSP00000554795.1

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68369 AN: 151380 Hom.: 15877 Cov.: 0

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.634

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.527

GnomAD2 exomes AF: 0.498 AC: 112310 AN: 225354 AF XY: 0.503

Gnomad AFR exome AF: 0.378

Gnomad AMR exome AF: 0.491

Gnomad ASJ exome AF: 0.613

Gnomad EAS exome AF: 0.649

Gnomad FIN exome AF: 0.366

Gnomad NFE exome AF: 0.492

Gnomad OTH exome AF: 0.513

GnomAD4 exome AF: 0.481 AC: 689382 AN: 1434038 Hom.: 168008 Cov.: 27 AF XY: 0.484 AC XY: 344003 AN XY: 711034

African (AFR) AF: 0.371 AC: 12023 AN: 32394

American (AMR) AF: 0.481 AC: 19940 AN: 41420

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 15016 AN: 24884

East Asian (EAS) AF: 0.648 AC: 25515 AN: 39382

South Asian (SAS) AF: 0.549 AC: 45067 AN: 82086

European-Finnish (FIN) AF: 0.375 AC: 19512 AN: 52024

Middle Eastern (MID) AF: 0.633 AC: 3564 AN: 5634

European-Non Finnish (NFE) AF: 0.473 AC: 519118 AN: 1097072

Other (OTH) AF: 0.501 AC: 29627 AN: 59142

GnomAD4 genome AF: 0.451 AC: 68390 AN: 151490 Hom.: 15874 Cov.: 0 AF XY: 0.448 AC XY: 33114 AN XY: 73970

African (AFR) AF: 0.373 AC: 15362 AN: 41210

American (AMR) AF: 0.480 AC: 7309 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 2077 AN: 3470

East Asian (EAS) AF: 0.633 AC: 3255 AN: 5140

South Asian (SAS) AF: 0.558 AC: 2686 AN: 4812

European-Finnish (FIN) AF: 0.351 AC: 3639 AN: 10382

Middle Eastern (MID) AF: 0.699 AC: 204 AN: 292

European-Non Finnish (NFE) AF: 0.477 AC: 32386 AN: 67928

Other (OTH) AF: 0.527 AC: 1111 AN: 2108

Alfa AF: 0.475 Hom.: 4253

Bravo AF: 0.460

Asia WGS AF: 0.598 AC: 2075 AN: 3474

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	Epilepsy, familial adult myoclonic, 4 (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.17
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3841649; hg19: chr3-183439972;