3-65341207-T-C

Variant names:

• chr3-65341207-T-C
• rs6764388

Variant summary

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

The variant allele was found at a frequency of 0.371 in 152,002 control chromosomes in the GnomAD database, including 12,734 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 0.37 (12734 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.429
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.478 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

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56395 AN: 151884 Hom.: 12720 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.371 AC: 56432 AN: 152002 Hom.: 12734 Cov.: 32 AF XY: 0.377 AC XY: 27980 AN XY: 74302

African (AFR) AF: 0.103 AC: 4275 AN: 41500

American (AMR) AF: 0.412 AC: 6278 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1374 AN: 3470

East Asian (EAS) AF: 0.492 AC: 2540 AN: 5160

South Asian (SAS) AF: 0.357 AC: 1720 AN: 4812

European-Finnish (FIN) AF: 0.572 AC: 6029 AN: 10548

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32773 AN: 67944

Other (OTH) AF: 0.385 AC: 813 AN: 2110

Alfa AF: 0.418 Hom.: 30091

Bravo AF: 0.347

Asia WGS AF: 0.411 AC: 1428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.26
DANN	Benign	0.42
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs6764388; hg19: chr3-65326882;