rs10518224

Variant names:

• chr4-79643354-G-A
• rs10518224

Your query was ambiguous. Multiple possible variants found:

• chr4-79643354-G-A
• chr4-79643354-G-C
• chr4-79643354-G-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 0.204 in 152,008 control chromosomes in the GnomAD database, including 3,864 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 0.20 (3864 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.722
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.275 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: 0.205 AC: 31097 AN: 151890 Hom.: 3866 Cov.: 32

Gnomad AFR AF: 0.0620

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.204 AC: 31079 AN: 152008 Hom.: 3864 Cov.: 32 AF XY: 0.207 AC XY: 15369 AN XY: 74276

African (AFR) AF: 0.0619 AC: 2569 AN: 41522

American (AMR) AF: 0.148 AC: 2255 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 608 AN: 3472

East Asian (EAS) AF: 0.285 AC: 1470 AN: 5152

South Asian (SAS) AF: 0.155 AC: 748 AN: 4826

European-Finnish (FIN) AF: 0.355 AC: 3746 AN: 10552

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.278 AC: 18909 AN: 67932

Other (OTH) AF: 0.191 AC: 402 AN: 2108

Alfa AF: 0.228 Hom.: 5330

Bravo AF: 0.184

Asia WGS AF: 0.180 AC: 625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.28
DANN	Benign	0.17
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs10518224; hg19: chr4-80564508;