chr6-4960186-C-T

Variant names:

• chr6-4960186-C-T
• rs2985678

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 0.826 in 152,128 control chromosomes in the GnomAD database, including 52,120 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 0.83 (52120 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.947
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.93 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: 0.827 AC: 125637 AN: 152010 Hom.: 52082 Cov.: 32

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.863

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.953

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.826 AC: 125730 AN: 152128 Hom.: 52120 Cov.: 32 AF XY: 0.828 AC XY: 61594 AN XY: 74366

African (AFR) AF: 0.767 AC: 31795 AN: 41476

American (AMR) AF: 0.863 AC: 13196 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.853 AC: 2962 AN: 3472

East Asian (EAS) AF: 0.953 AC: 4933 AN: 5178

South Asian (SAS) AF: 0.881 AC: 4246 AN: 4822

European-Finnish (FIN) AF: 0.823 AC: 8691 AN: 10558

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.839 AC: 57091 AN: 68018

Other (OTH) AF: 0.845 AC: 1784 AN: 2112

Alfa AF: 0.841 Hom.: 59096

Bravo AF: 0.826

Asia WGS AF: 0.918 AC: 3190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.45
DANN	Benign	0.39
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs2985678; hg19: chr6-4960420;