rs4960155

Positions:

• chr6-6010306-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 0.573 in 152,056 control chromosomes in the GnomAD database, including 26,082 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 0.57 (26082 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.745 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: 0.573 AC: 87110 AN: 151940 Hom.: 26052 Cov.: 32

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.573 AC: 87185 AN: 152056 Hom.: 26082 Cov.: 32 AF XY: 0.566 AC XY: 42059 AN XY: 74310

Gnomad4 AFR AF: 0.752

Gnomad4 AMR AF: 0.510

Gnomad4 ASJ AF: 0.538

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.456

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.544

Alfa AF: 0.525 Hom.: 43160

Bravo AF: 0.587

Asia WGS AF: 0.495 AC: 1722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.8
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4960155; hg19: chr6-6010539;