3-62897705-C-T

Variant names:

• chr3-62897705-C-T
• rs1992192
• ENST00000761991.1:n.248+1320G>A

Variant summary

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

The ENST00000761991.1(ENSG00000299258):​n.248+1320G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 151,978 control chromosomes in the GnomAD database, including 9,442 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 0.34 (9442 hom., cov: 32)
• Consequence: ENSG00000299258 ENST00000761991.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.300
• Publications: 6 publications found

Genes affected

ENSG00000299258 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000761991.1. 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
	ENSG00000299258	ENST00000761991.1		n.248+1320G>A		intron	N/A
	ENSG00000299258	ENST00000761992.1		n.90+1320G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51061 AN: 151860 Hom.: 9418 Cov.: 32

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.337 AC: 51143 AN: 151978 Hom.: 9442 Cov.: 32 AF XY: 0.339 AC XY: 25162 AN XY: 74304

African (AFR) AF: 0.492 AC: 20407 AN: 41440

American (AMR) AF: 0.368 AC: 5607 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 759 AN: 3464

East Asian (EAS) AF: 0.387 AC: 1999 AN: 5160

South Asian (SAS) AF: 0.305 AC: 1470 AN: 4816

European-Finnish (FIN) AF: 0.293 AC: 3099 AN: 10588

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16746 AN: 67938

Other (OTH) AF: 0.308 AC: 649 AN: 2110

Alfa AF: 0.270 Hom.: 11355

Bravo AF: 0.355

Asia WGS AF: 0.311 AC: 1081 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.6
DANN	Benign	0.40
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs1992192; hg19: chr3-62883380;