3-65341207-T-C

Position:

• chr3-65341207-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;