chr4-179363660-T-C

Variant names:

• chr4-179363660-T-C
• rs6811556

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 0.561 in 151,886 control chromosomes in the GnomAD database, including 24,444 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 0.56 (24444 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.636 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: 0.561 AC: 85166 AN: 151770 Hom.: 24447 Cov.: 31

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.561 AC: 85180 AN: 151886 Hom.: 24444 Cov.: 31 AF XY: 0.554 AC XY: 41107 AN XY: 74232

African (AFR) AF: 0.473 AC: 19616 AN: 41440

American (AMR) AF: 0.507 AC: 7728 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2208 AN: 3460

East Asian (EAS) AF: 0.346 AC: 1776 AN: 5136

South Asian (SAS) AF: 0.524 AC: 2524 AN: 4820

European-Finnish (FIN) AF: 0.564 AC: 5947 AN: 10542

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.641 AC: 43531 AN: 67938

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

Alfa AF: 0.591 Hom.: 22838

Bravo AF: 0.550

Asia WGS AF: 0.445 AC: 1550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.37
DANN	Benign	0.59
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6811556; hg19: chr4-180284814;