6-80960444-C-T

Variant names:

• chr6-80960444-C-T
• rs7770832

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 0.365 in 151,462 control chromosomes in the GnomAD database, including 10,176 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 0.36 (10176 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.539 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: 0.364 AC: 55152 AN: 151342 Hom.: 10148 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.365 AC: 55221 AN: 151462 Hom.: 10176 Cov.: 32 AF XY: 0.369 AC XY: 27316 AN XY: 73972

African (AFR) AF: 0.371 AC: 15376 AN: 41390

American (AMR) AF: 0.304 AC: 4603 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1129 AN: 3460

East Asian (EAS) AF: 0.557 AC: 2835 AN: 5094

South Asian (SAS) AF: 0.429 AC: 2062 AN: 4812

European-Finnish (FIN) AF: 0.403 AC: 4246 AN: 10532

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23822 AN: 67708

Other (OTH) AF: 0.359 AC: 753 AN: 2100

Alfa AF: 0.349 Hom.: 1501

Bravo AF: 0.356

Asia WGS AF: 0.455 AC: 1577 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.5
DANN	Benign	0.28
PhyloP100		-0.014

Splicing

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

Other links and lift over

dbSNP: rs7770832; hg19: chr6-81670161;