rs1979797

Variant names:

• chr6-91783152-C-T
• rs1979797

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;