rs4960155

Variant names:

• chr6-6010306-C-T
• rs4960155

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 0.573 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.752 AC: 31177 AN: 41482

American (AMR) AF: 0.510 AC: 7804 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1867 AN: 3470

East Asian (EAS) AF: 0.498 AC: 2569 AN: 5162

South Asian (SAS) AF: 0.454 AC: 2187 AN: 4818

European-Finnish (FIN) AF: 0.456 AC: 4806 AN: 10544

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.514 AC: 34907 AN: 67970

Other (OTH) AF: 0.544 AC: 1148 AN: 2110

Alfa AF: 0.536 Hom.: 69843

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
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs4960155; hg19: chr6-6010539;