rs6537835

chr1-114566293-G-Achr1-114566293-G-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 0.798 in 152,014 control chromosomes in the GnomAD database, including 49,751 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 0.80 (49751 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320

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 (NFE) allele frequency at 95% confidence interval = 0.914 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: 0.799 AC: 121318 AN: 151896 Hom.: 49739 Cov.: 33

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.872

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.893

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.822

Gnomad NFE AF: 0.920

Gnomad OTH AF: 0.809

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

GnomAD4 genome AF: 0.798 AC: 121375 AN: 152014 Hom.: 49751 Cov.: 33 AF XY: 0.790 AC XY: 58716 AN XY: 74286

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.759

Gnomad4 ASJ AF: 0.893

Gnomad4 EAS AF: 0.587

Gnomad4 SAS AF: 0.622

Gnomad4 FIN AF: 0.812

Gnomad4 NFE AF: 0.920

Gnomad4 OTH AF: 0.805

Alfa AF: 0.872 Hom.: 11870

Bravo AF: 0.789

Asia WGS AF: 0.599 AC: 2087 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	3.8
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6537835; hg19: chr1-115108914;