4-87935581-C-T

Variant names:

• chr4-87935581-C-T
• rs10516796

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 0.552 in 151,968 control chromosomes in the GnomAD database, including 23,776 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 0.55 (23776 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.651 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: 0.553 AC: 83915 AN: 151850 Hom.: 23772 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.659

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.552 AC: 83948 AN: 151968 Hom.: 23776 Cov.: 32 AF XY: 0.558 AC XY: 41426 AN XY: 74270

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.682

Gnomad4 EAS AF: 0.634

Gnomad4 SAS AF: 0.670

Gnomad4 FIN AF: 0.655

Gnomad4 NFE AF: 0.595

Gnomad4 OTH AF: 0.562

Alfa AF: 0.591 Hom.: 12207

Bravo AF: 0.538

Asia WGS AF: 0.631 AC: 2194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516796; hg19: chr4-88856733;