2-62332070-T-C

Variant names:

• chr2-62332070-T-C
• rs6759003
• ENST00000687402.3:n.199+35624T>C

Variant summary

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

The ENST00000687402.3(ENSG00000228541):​n.199+35624T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 151,278 control chromosomes in the GnomAD database, including 25,981 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 0.58 (25981 hom., cov: 27)
• Consequence: ENSG00000228541 ENST00000687402.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 10 publications found

Genes affected

ENSG00000228541 (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 = 0.65 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
ENSG00000228541	ENST00000687402.3	n.199+35624T>C		intron_variant	Intron 1 of 1
ENSG00000228541	ENST00000687773.2	n.200-29750T>C		intron_variant	Intron 1 of 1
ENSG00000228541	ENST00000688476.3	n.202-13844T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.581 AC: 87820 AN: 151160 Hom.: 25954 Cov.: 27

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.581 AC: 87909 AN: 151278 Hom.: 25981 Cov.: 27 AF XY: 0.584 AC XY: 43188 AN XY: 73904

African (AFR) AF: 0.463 AC: 19040 AN: 41146

American (AMR) AF: 0.604 AC: 9168 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.585 AC: 2026 AN: 3462

East Asian (EAS) AF: 0.587 AC: 2994 AN: 5098

South Asian (SAS) AF: 0.669 AC: 3199 AN: 4782

European-Finnish (FIN) AF: 0.653 AC: 6838 AN: 10474

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.630 AC: 42740 AN: 67848

Other (OTH) AF: 0.572 AC: 1199 AN: 2096

Alfa AF: 0.602 Hom.: 8053

Bravo AF: 0.570

Asia WGS AF: 0.618 AC: 2151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.35
DANN	Benign	0.74
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs6759003; hg19: chr2-62559205;