rs10017136

Variant names:

• chr4-99377524-A-C
• rs10017136

Your query was ambiguous. Multiple possible variants found:

• chr4-99377524-A-C
• chr4-99377524-A-G
• chr4-99377524-A-T

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 0.25 in 150,790 control chromosomes in the GnomAD database, including 5,510 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 0.25 (5510 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.655 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: 0.250 AC: 37730 AN: 150696 Hom.: 5503 Cov.: 31

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.250 AC: 37764 AN: 150790 Hom.: 5510 Cov.: 31 AF XY: 0.257 AC XY: 18925 AN XY: 73514

African (AFR) AF: 0.308 AC: 12643 AN: 41008

American (AMR) AF: 0.183 AC: 2776 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 608 AN: 3456

East Asian (EAS) AF: 0.674 AC: 3436 AN: 5098

South Asian (SAS) AF: 0.468 AC: 2243 AN: 4792

European-Finnish (FIN) AF: 0.173 AC: 1761 AN: 10166

Middle Eastern (MID) AF: 0.210 AC: 60 AN: 286

European-Non Finnish (NFE) AF: 0.199 AC: 13513 AN: 67812

Other (OTH) AF: 0.235 AC: 492 AN: 2090

Alfa AF: 0.215 Hom.: 927

Bravo AF: 0.250

Asia WGS AF: 0.469 AC: 1629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.5
DANN	Benign	0.54
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs10017136; hg19: chr4-100298681;