6-51101004-C-T

Variant names:

• chr6-51101004-C-T
• rs7775861

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 0.323 in 151,922 control chromosomes in the GnomAD database, including 8,721 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 0.32 (8721 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.393 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: 0.323 AC: 49010 AN: 151804 Hom.: 8722 Cov.: 31

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.323 AC: 49018 AN: 151922 Hom.: 8721 Cov.: 31 AF XY: 0.320 AC XY: 23749 AN XY: 74236

African (AFR) AF: 0.184 AC: 7642 AN: 41478

American (AMR) AF: 0.397 AC: 6055 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1032 AN: 3468

East Asian (EAS) AF: 0.219 AC: 1127 AN: 5152

South Asian (SAS) AF: 0.355 AC: 1707 AN: 4808

European-Finnish (FIN) AF: 0.331 AC: 3494 AN: 10550

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 26978 AN: 67922

Other (OTH) AF: 0.300 AC: 631 AN: 2102

Alfa AF: 0.350 Hom.: 9208

Bravo AF: 0.322

Asia WGS AF: 0.317 AC: 1104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.17
DANN	Benign	0.67
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs7775861; hg19: chr6-51068717;