rs6540431

Variant names:

• chr1-206468531-G-C
• rs6540431

Your query was ambiguous. Multiple possible variants found:

• chr1-206468531-G-C
• chr1-206468531-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.955 in 152,216 control chromosomes in the GnomAD database, including 69,489 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 0.96 (69489 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.979 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: 0.955 AC: 145254 AN: 152098 Hom.: 69424 Cov.: 34

Gnomad AFR AF: 0.987

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.961

Gnomad ASJ AF: 0.902

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.980

Gnomad FIN AF: 0.967

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.930

Gnomad OTH AF: 0.949

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

GnomAD4 genome AF: 0.955 AC: 145378 AN: 152216 Hom.: 69489 Cov.: 34 AF XY: 0.958 AC XY: 71257 AN XY: 74396

African (AFR) AF: 0.987 AC: 41010 AN: 41558

American (AMR) AF: 0.961 AC: 14700 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.902 AC: 3130 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5186 AN: 5186

South Asian (SAS) AF: 0.980 AC: 4736 AN: 4832

European-Finnish (FIN) AF: 0.967 AC: 10234 AN: 10582

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.930 AC: 63210 AN: 67972

Other (OTH) AF: 0.950 AC: 2002 AN: 2108

Alfa AF: 0.945 Hom.: 8451

Bravo AF: 0.956

Asia WGS AF: 0.986 AC: 3427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.67
DANN	Benign	0.70
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs6540431; hg19: chr1-206641874;