chr6-80696852-T-C

Variant names:

• chr6-80696852-T-C
• rs1377986

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 0.552 in 151,884 control chromosomes in the GnomAD database, including 24,396 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 0.55 (24396 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.703 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: 0.552 AC: 83795 AN: 151766 Hom.: 24396 Cov.: 31

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.552 AC: 83819 AN: 151884 Hom.: 24396 Cov.: 31 AF XY: 0.553 AC XY: 41043 AN XY: 74214

African (AFR) AF: 0.347 AC: 14380 AN: 41412

American (AMR) AF: 0.620 AC: 9435 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2214 AN: 3470

East Asian (EAS) AF: 0.723 AC: 3711 AN: 5136

South Asian (SAS) AF: 0.461 AC: 2222 AN: 4820

European-Finnish (FIN) AF: 0.694 AC: 7326 AN: 10556

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.627 AC: 42597 AN: 67942

Other (OTH) AF: 0.589 AC: 1244 AN: 2112

Alfa AF: 0.591 Hom.: 5566

Bravo AF: 0.541

Asia WGS AF: 0.583 AC: 2025 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	2.5
DANN	Benign	0.65
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs1377986; hg19: chr6-81406569;