4-29938472-T-C

Variant names:

• chr4-29938472-T-C
• rs6811604

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 0.433 in 151,738 control chromosomes in the GnomAD database, including 19,310 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 0.43 (19310 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.900
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65640 AN: 151620 Hom.: 19256 Cov.: 32

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.442

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.433 AC: 65751 AN: 151738 Hom.: 19310 Cov.: 32 AF XY: 0.424 AC XY: 31440 AN XY: 74182

African (AFR) AF: 0.842 AC: 34820 AN: 41334

American (AMR) AF: 0.275 AC: 4185 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1214 AN: 3466

East Asian (EAS) AF: 0.449 AC: 2305 AN: 5132

South Asian (SAS) AF: 0.345 AC: 1660 AN: 4812

European-Finnish (FIN) AF: 0.209 AC: 2208 AN: 10554

Middle Eastern (MID) AF: 0.449 AC: 131 AN: 292

European-Non Finnish (NFE) AF: 0.268 AC: 18178 AN: 67900

Other (OTH) AF: 0.420 AC: 887 AN: 2110

Alfa AF: 0.364 Hom.: 2246

Bravo AF: 0.458

Asia WGS AF: 0.423 AC: 1476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.91
DANN	Benign	0.71
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs6811604; hg19: chr4-29940094;