chr4-156430090-T-C

Variant names:

• chr4-156430090-T-C
• rs10517636

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.427 in 151,860 control chromosomes in the GnomAD database, including 14,638 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 (14638 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 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: 0.427 AC: 64754 AN: 151740 Hom.: 14618 Cov.: 31

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.427 AC: 64819 AN: 151860 Hom.: 14638 Cov.: 31 AF XY: 0.422 AC XY: 31286 AN XY: 74222

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.414

Alfa AF: 0.395 Hom.: 24538

Bravo AF: 0.429

Asia WGS AF: 0.242 AC: 845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.0
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517636; hg19: chr4-157351242;