rs10518025

Variant names:

• chr4-67198722-T-C
• rs10518025

Your query was ambiguous. Multiple possible variants found:

• chr4-67198722-T-C
• chr4-67198722-T-G

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 0.144 in 152,176 control chromosomes in the GnomAD database, including 1,669 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 0.14 (1669 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.792

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.165 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: 0.144 AC: 21850 AN: 152058 Hom.: 1669 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0787

Gnomad EAS AF: 0.0868

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.144 AC: 21866 AN: 152176 Hom.: 1669 Cov.: 32 AF XY: 0.143 AC XY: 10643 AN XY: 74402

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.0787

Gnomad4 EAS AF: 0.0858

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.131

Alfa AF: 0.136 Hom.: 3202

Bravo AF: 0.141

Asia WGS AF: 0.160 AC: 554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	9.1
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10518025; hg19: chr4-68064440;