NM_001372053.1:c.3596-1929G>T

Variant names:

• chr5-75140912-C-A
• rs1600073
• NM_001372053.1:c.3596-1929G>T

Variant summary

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

The NM_001372053.1(ANKRD31):​c.3596-1929G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0489 in 152,114 control chromosomes in the GnomAD database, including 398 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 0.049 (398 hom., cov: 32)
• Consequence: ANKRD31 NM_001372053.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280
• Publications: 0 publications found

Genes affected

ANKRD31 (HGNC:26853): (ankyrin repeat domain 31) This gene encodes a protein containing multiple ankyrin repeats. Ankyrin domains function in protein-protein interactions in a variety of cellular processes. Mutations in this gene are associated with a Rett syndrome (RTT)-like phenotype. [provided by RefSeq, Apr 2017]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001372053.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD31	NM_001372053.1	MANE Select	c.3596-1929G>T		intron	N/A	NP_001358982.1
	ANKRD31	NM_001164443.1		c.3425-1929G>T		intron	N/A	NP_001157915.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD31	ENST00000506364.6	TSL:5 MANE Select	c.3596-1929G>T		intron	N/A	ENSP00000427262.2
	ANKRD31	ENST00000274361.3	TSL:5	c.3425-1929G>T		intron	N/A	ENSP00000274361.3
	ANKRD31	ENST00000504022.1	TSL:5	n.386-1929G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0488 AC: 7419 AN: 151996 Hom.: 397 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0295

Gnomad ASJ AF: 0.0158

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.00331

Gnomad FIN AF: 0.00927

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0187

Gnomad OTH AF: 0.0523

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

GnomAD4 genome AF: 0.0489 AC: 7440 AN: 152114 Hom.: 398 Cov.: 32 AF XY: 0.0466 AC XY: 3463 AN XY: 74348

African (AFR) AF: 0.131 AC: 5418 AN: 41516

American (AMR) AF: 0.0294 AC: 450 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0158 AC: 55 AN: 3472

East Asian (EAS) AF: 0.000388 AC: 2 AN: 5158

South Asian (SAS) AF: 0.00332 AC: 16 AN: 4824

European-Finnish (FIN) AF: 0.00927 AC: 98 AN: 10568

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0188 AC: 1275 AN: 67978

Other (OTH) AF: 0.0513 AC: 108 AN: 2106

Alfa AF: 0.00668 Hom.: 346

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.88
DANN	Benign	0.46
PhyloP100		-0.28
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: rs1600073; hg19: chr5-74436737;