rs1979797

chr6-91783152-C-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 0.404 in 151,754 control chromosomes in the GnomAD database, including 13,470 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 0.40 (13470 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.58

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 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: 0.404 AC: 61247 AN: 151638 Hom.: 13432 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.404 AC: 61339 AN: 151754 Hom.: 13470 Cov.: 32 AF XY: 0.406 AC XY: 30052 AN XY: 74100

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.386

Alfa AF: 0.352 Hom.: 2024

Bravo AF: 0.416

Asia WGS AF: 0.374 AC: 1302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.012
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1979797; hg19: chr6-92492870;