rs6781977

Positions:

• chr3-143206165-G-A
• chr3-143206165-G-T

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 0.642 in 151,948 control chromosomes in the GnomAD database, including 31,700 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 0.64 (31700 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.612

ACMG classification

Verdict is Benign. Variant got -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 = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97494 AN: 151830 Hom.: 31671 Cov.: 31

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.642 AC: 97572 AN: 151948 Hom.: 31700 Cov.: 31 AF XY: 0.638 AC XY: 47340 AN XY: 74258

Gnomad4 AFR AF: 0.699

Gnomad4 AMR AF: 0.626

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.568

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.667

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.623

Alfa AF: 0.625 Hom.: 14451

Bravo AF: 0.647

Asia WGS AF: 0.483 AC: 1683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.64
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6781977; hg19: chr3-142925007;