chr2-62579956-A-C

Variant names:

• chr2-62579956-A-C
• rs1406002
• ENST00000664749.1:n.288+10545T>G

Variant summary

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

The ENST00000664749.1(ENSG00000226622):​n.288+10545T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 152,024 control chromosomes in the GnomAD database, including 29,955 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 (29955 hom., cov: 32)
• Consequence: ENSG00000226622 ENST00000664749.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277
• Publications: 2 publications found

Genes affected

ENSG00000226622 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.721 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664749.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226622	ENST00000664749.1		n.288+10545T>G		intron	N/A
	ENSG00000226622	ENST00000668814.1		n.305-1312T>G		intron	N/A
	ENSG00000228541	ENST00000807713.1		n.400+16091A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94614 AN: 151906 Hom.: 29936 Cov.: 32

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.623 AC: 94684 AN: 152024 Hom.: 29955 Cov.: 32 AF XY: 0.622 AC XY: 46187 AN XY: 74306

African (AFR) AF: 0.728 AC: 30176 AN: 41478

American (AMR) AF: 0.611 AC: 9341 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1781 AN: 3466

East Asian (EAS) AF: 0.672 AC: 3478 AN: 5178

South Asian (SAS) AF: 0.560 AC: 2699 AN: 4816

European-Finnish (FIN) AF: 0.598 AC: 6302 AN: 10546

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.572 AC: 38892 AN: 67948

Other (OTH) AF: 0.614 AC: 1294 AN: 2106

Alfa AF: 0.547 Hom.: 17383

Bravo AF: 0.632

Asia WGS AF: 0.667 AC: 2314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.36
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1406002; hg19: chr2-62807091;