3-65341207-T-C

Variant names:

• chr3-65341207-T-C
• rs6764388

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.572

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.385

Alfa AF: 0.450 Hom.: 21117

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6764388; hg19: chr3-65326882;