4-34371405-C-T

Variant names:

• chr4-34371405-C-T
• rs10517306

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 0.217 in 127,518 control chromosomes in the GnomAD database, including 4,101 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 0.22 (4101 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.47
• 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 = 0.461 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: 0.217 AC: 27632 AN: 127426 Hom.: 4102 Cov.: 30

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.0345

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.00462

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.217 AC: 27648 AN: 127518 Hom.: 4101 Cov.: 30 AF XY: 0.216 AC XY: 13343 AN XY: 61740

African (AFR) AF: 0.467 AC: 17088 AN: 36564

American (AMR) AF: 0.144 AC: 1633 AN: 11366

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 364 AN: 3210

East Asian (EAS) AF: 0.00462 AC: 15 AN: 3250

South Asian (SAS) AF: 0.233 AC: 880 AN: 3774

European-Finnish (FIN) AF: 0.118 AC: 983 AN: 8314

Middle Eastern (MID) AF: 0.137 AC: 35 AN: 256

European-Non Finnish (NFE) AF: 0.108 AC: 6284 AN: 58116

Other (OTH) AF: 0.187 AC: 336 AN: 1798

Alfa AF: 0.104 Hom.: 1124

Bravo AF: 0.192

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.030
DANN	Benign	0.57
PhyloP100		-4.5

Splicing

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

Other links and lift over

dbSNP: rs10517306; hg19: chr4-34373027;