4-136605429-T-C

Variant names:

• chr4-136605429-T-C
• rs10012307

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 0.214 in 152,040 control chromosomes in the GnomAD database, including 6,131 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 0.21 (6131 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.589
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 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: 0.214 AC: 32511 AN: 151922 Hom.: 6120 Cov.: 32

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.0637

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0560

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.0708

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.214 AC: 32565 AN: 152040 Hom.: 6131 Cov.: 32 AF XY: 0.217 AC XY: 16116 AN XY: 74330

African (AFR) AF: 0.501 AC: 20754 AN: 41456

American (AMR) AF: 0.129 AC: 1975 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0560 AC: 194 AN: 3466

East Asian (EAS) AF: 0.379 AC: 1956 AN: 5162

South Asian (SAS) AF: 0.135 AC: 651 AN: 4828

European-Finnish (FIN) AF: 0.164 AC: 1738 AN: 10570

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.0708 AC: 4811 AN: 67972

Other (OTH) AF: 0.181 AC: 383 AN: 2114

Alfa AF: 0.171 Hom.: 3434

Bravo AF: 0.225

Asia WGS AF: 0.241 AC: 838 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.79
DANN	Benign	0.82
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs10012307; hg19: chr4-137526584;