chr6-43796814-C-T

Variant names:

• chr6-43796814-C-T
• rs1358980

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 0.406 in 151,898 control chromosomes in the GnomAD database, including 14,348 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 0.41 (14348 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.334
• Publications: 63 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.651 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: 0.406 AC: 61589 AN: 151780 Hom.: 14337 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.406 AC: 61619 AN: 151898 Hom.: 14348 Cov.: 32 AF XY: 0.413 AC XY: 30691 AN XY: 74230

African (AFR) AF: 0.167 AC: 6917 AN: 41406

American (AMR) AF: 0.499 AC: 7627 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1841 AN: 3468

East Asian (EAS) AF: 0.545 AC: 2811 AN: 5158

South Asian (SAS) AF: 0.670 AC: 3234 AN: 4824

European-Finnish (FIN) AF: 0.480 AC: 5051 AN: 10528

Middle Eastern (MID) AF: 0.507 AC: 148 AN: 292

European-Non Finnish (NFE) AF: 0.479 AC: 32520 AN: 67928

Other (OTH) AF: 0.432 AC: 908 AN: 2104

Alfa AF: 0.460 Hom.: 72467

Bravo AF: 0.392

Asia WGS AF: 0.536 AC: 1864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	11
DANN	Benign	0.77
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs1358980; hg19: chr6-43764551;