chr6-4960186-C-T

Variant names:

• chr6-4960186-C-T
• rs2985678

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 0.826 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.767

Gnomad4 AMR AF: 0.863

Gnomad4 ASJ AF: 0.853

Gnomad4 EAS AF: 0.953

Gnomad4 SAS AF: 0.881

Gnomad4 FIN AF: 0.823

Gnomad4 NFE AF: 0.839

Gnomad4 OTH AF: 0.845

Alfa AF: 0.843 Hom.: 49524

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2985678; hg19: chr6-4960420;