4-153453832-T-C

Variant names:

• chr4-153453832-T-C
• rs6817170

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 0.344 in 152,076 control chromosomes in the GnomAD database, including 9,917 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 0.34 (9917 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0520
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52303 AN: 151958 Hom.: 9902 Cov.: 32

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.344 AC: 52358 AN: 152076 Hom.: 9917 Cov.: 32 AF XY: 0.348 AC XY: 25842 AN XY: 74330

African (AFR) AF: 0.503 AC: 20862 AN: 41470

American (AMR) AF: 0.219 AC: 3347 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 722 AN: 3466

East Asian (EAS) AF: 0.329 AC: 1701 AN: 5172

South Asian (SAS) AF: 0.462 AC: 2225 AN: 4812

European-Finnish (FIN) AF: 0.338 AC: 3582 AN: 10582

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.278 AC: 18885 AN: 67972

Other (OTH) AF: 0.323 AC: 683 AN: 2116

Alfa AF: 0.290 Hom.: 9471

Bravo AF: 0.339

Asia WGS AF: 0.426 AC: 1482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.5
DANN	Benign	0.35
PhyloP100		-0.052

Splicing

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

Other links and lift over

dbSNP: rs6817170; hg19: chr4-154374984;