rs4960166

Variant names:

• chr6-6136412-A-G
• rs4960166

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 0.255 in 152,080 control chromosomes in the GnomAD database, including 5,465 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 0.26 (5465 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.361 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: 0.255 AC: 38801 AN: 151964 Hom.: 5456 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.255 AC: 38848 AN: 152080 Hom.: 5465 Cov.: 32 AF XY: 0.249 AC XY: 18506 AN XY: 74340

African (AFR) AF: 0.366 AC: 15155 AN: 41448

American (AMR) AF: 0.232 AC: 3539 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 919 AN: 3472

East Asian (EAS) AF: 0.103 AC: 533 AN: 5186

South Asian (SAS) AF: 0.206 AC: 994 AN: 4816

European-Finnish (FIN) AF: 0.157 AC: 1658 AN: 10592

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15310 AN: 67976

Other (OTH) AF: 0.256 AC: 540 AN: 2110

Alfa AF: 0.244 Hom.: 1682

Bravo AF: 0.265

Asia WGS AF: 0.150 AC: 526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.9
DANN	Benign	0.74
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs4960166; hg19: chr6-6136645;