rs681442

chr6-150415624-C-Gchr6-150415624-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 0.895 in 152,244 control chromosomes in the GnomAD database, including 61,151 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 0.90 (61151 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.924 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: 0.896 AC: 136251 AN: 152126 Hom.: 61123 Cov.: 33

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.906

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.830

Gnomad FIN AF: 0.898

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.916

Gnomad OTH AF: 0.899

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

GnomAD4 genome AF: 0.895 AC: 136330 AN: 152244 Hom.: 61151 Cov.: 33 AF XY: 0.894 AC XY: 66527 AN XY: 74432

Gnomad4 AFR AF: 0.856

Gnomad4 AMR AF: 0.937

Gnomad4 ASJ AF: 0.896

Gnomad4 EAS AF: 0.868

Gnomad4 SAS AF: 0.830

Gnomad4 FIN AF: 0.898

Gnomad4 NFE AF: 0.916

Gnomad4 OTH AF: 0.899

Alfa AF: 0.906 Hom.: 7736

Bravo AF: 0.899

Asia WGS AF: 0.846 AC: 2945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.24
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs681442; hg19: chr6-150736760; COSMIC: COSV69430292;