chr2-62578767-T-C

Variant names:

• chr2-62578767-T-C
• rs10496099
• ENST00000664749.1:n.288+11734A>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+11734A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.671 in 152,066 control chromosomes in the GnomAD database, including 34,490 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 0.67 (34490 hom., cov: 32)
• Consequence: ENSG00000226622 ENST00000664749.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45
• Publications: 5 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226622	ENST00000664749.1	n.288+11734A>G		intron_variant	Intron 3 of 3
ENSG00000226622	ENST00000668814.1	n.305-123A>G		intron_variant	Intron 4 of 4
ENSG00000228541	ENST00000807713.1	n.400+14902T>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.671 AC: 101965 AN: 151948 Hom.: 34460 Cov.: 32

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.671 AC: 102053 AN: 152066 Hom.: 34490 Cov.: 32 AF XY: 0.669 AC XY: 49695 AN XY: 74336

African (AFR) AF: 0.741 AC: 30713 AN: 41474

American (AMR) AF: 0.643 AC: 9823 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1966 AN: 3466

East Asian (EAS) AF: 0.730 AC: 3776 AN: 5174

South Asian (SAS) AF: 0.648 AC: 3122 AN: 4818

European-Finnish (FIN) AF: 0.643 AC: 6794 AN: 10562

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.643 AC: 43682 AN: 67970

Other (OTH) AF: 0.655 AC: 1383 AN: 2112

Alfa AF: 0.648 Hom.: 13879

Bravo AF: 0.677

Asia WGS AF: 0.736 AC: 2560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	10
DANN	Benign	0.62
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs10496099; hg19: chr2-62805902;