4-66559244-C-T

Variant names:

• chr4-66559244-C-T
• rs10517986

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 0.104 in 152,110 control chromosomes in the GnomAD database, including 2,305 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 0.10 (2305 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.322 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: 0.104 AC: 15732 AN: 151990 Hom.: 2294 Cov.: 33

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0715

Gnomad ASJ AF: 0.0334

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0118

Gnomad FIN AF: 0.00821

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00921

Gnomad OTH AF: 0.0927

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

GnomAD4 genome AF: 0.104 AC: 15771 AN: 152110 Hom.: 2305 Cov.: 33 AF XY: 0.100 AC XY: 7452 AN XY: 74394

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.0713

Gnomad4 ASJ AF: 0.0334

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0116

Gnomad4 FIN AF: 0.00821

Gnomad4 NFE AF: 0.00921

Gnomad4 OTH AF: 0.0918

Alfa AF: 0.0310 Hom.: 183

Bravo AF: 0.118

Asia WGS AF: 0.0280 AC: 99 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.070
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517986; hg19: chr4-67424962;