chr5-75184463-T-C

Variant names:

• chr5-75184463-T-C
• rs4704187
• NM_001372053.1:c.1564+4030A>G

Variant summary

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

The NM_001372053.1(ANKRD31):​c.1564+4030A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 151,992 control chromosomes in the GnomAD database, including 31,862 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 0.62 (31862 hom., cov: 32)
• Consequence: ANKRD31 NM_001372053.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 4 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD31	NM_001372053.1	c.1564+4030A>G		intron_variant	Intron 10 of 25	ENST00000506364.6	NP_001358982.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD31	ENST00000506364.6	c.1564+4030A>G		intron_variant	Intron 10 of 25	5	NM_001372053.1	ENSP00000427262.2
ANKRD31	ENST00000274361.3	c.1564+4030A>G		intron_variant	Intron 10 of 24	5		ENSP00000274361.3
ANKRD31	ENST00000674120.1	n.*781+4030A>G		intron_variant	Intron 7 of 21			ENSP00000501032.1

Frequencies

GnomAD3 genomes AF: 0.620 AC: 94180 AN: 151874 Hom.: 31795 Cov.: 32

Gnomad AFR AF: 0.904

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.621 AC: 94313 AN: 151992 Hom.: 31862 Cov.: 32 AF XY: 0.623 AC XY: 46303 AN XY: 74290

African (AFR) AF: 0.904 AC: 37533 AN: 41498

American (AMR) AF: 0.553 AC: 8437 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1734 AN: 3466

East Asian (EAS) AF: 0.698 AC: 3612 AN: 5176

South Asian (SAS) AF: 0.602 AC: 2898 AN: 4814

European-Finnish (FIN) AF: 0.551 AC: 5803 AN: 10526

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32389 AN: 67948

Other (OTH) AF: 0.586 AC: 1235 AN: 2108

Alfa AF: 0.546 Hom.: 32465

Bravo AF: 0.633

Asia WGS AF: 0.683 AC: 2364 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.9
DANN	Benign	0.62
PhyloP100		-0.93
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: rs4704187; hg19: chr5-74480288;