2-223840189-G-A

Variant names:

• chr2-223840189-G-A
• rs6436440
• ENST00000650969.1:n.*967+15589C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650969.1(ENSG00000286239):​n.*967+15589C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 140,748 control chromosomes in the GnomAD database, including 15,959 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.48 (15959 hom., cov: 21)
• Consequence: ENSG00000286239 ENST00000650969.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.313
• Publications: 5 publications found

Genes affected

ENSG00000286239 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650969.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286239	ENST00000650969.1		n.*967+15589C>T		intron	N/A	ENSP00000498456.1	A0A494C0A6

Frequencies

GnomAD3 genomes AF: 0.480 AC: 67477 AN: 140654 Hom.: 15953 Cov.: 21

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.479

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.480 AC: 67503 AN: 140748 Hom.: 15959 Cov.: 21 AF XY: 0.482 AC XY: 32588 AN XY: 67652

African (AFR) AF: 0.462 AC: 17122 AN: 37076

American (AMR) AF: 0.515 AC: 6920 AN: 13446

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 1990 AN: 3392

East Asian (EAS) AF: 0.472 AC: 2258 AN: 4786

South Asian (SAS) AF: 0.536 AC: 2289 AN: 4272

European-Finnish (FIN) AF: 0.433 AC: 3876 AN: 8942

Middle Eastern (MID) AF: 0.578 AC: 156 AN: 270

European-Non Finnish (NFE) AF: 0.478 AC: 31466 AN: 65816

Other (OTH) AF: 0.478 AC: 889 AN: 1860

Alfa AF: 0.382 Hom.: 1466

Bravo AF: 0.480

Asia WGS AF: 0.488 AC: 1696 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.55
PhyloP100		-0.31

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6436440;

hg19: chr2-224704906;