rs10518309

Variant names:

• chr4-119069287-A-C
• rs10518309

Your query was ambiguous. Multiple possible variants found:

• chr4-119069287-A-C
• chr4-119069287-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 0.046 in 151,978 control chromosomes in the GnomAD database, including 413 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 0.046 (413 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.935
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 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: 0.0460 AC: 6985 AN: 151860 Hom.: 410 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0304

Gnomad ASJ AF: 0.0107

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.0353

Gnomad FIN AF: 0.00142

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.00287

Gnomad OTH AF: 0.0470

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

GnomAD4 genome AF: 0.0460 AC: 6990 AN: 151978 Hom.: 413 Cov.: 32 AF XY: 0.0460 AC XY: 3418 AN XY: 74312

African (AFR) AF: 0.130 AC: 5387 AN: 41470

American (AMR) AF: 0.0303 AC: 462 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.0107 AC: 37 AN: 3468

East Asian (EAS) AF: 0.120 AC: 616 AN: 5146

South Asian (SAS) AF: 0.0349 AC: 168 AN: 4818

European-Finnish (FIN) AF: 0.00142 AC: 15 AN: 10544

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.00287 AC: 195 AN: 67990

Other (OTH) AF: 0.0470 AC: 99 AN: 2106

Alfa AF: 0.00749 Hom.: 6

Bravo AF: 0.0510

Asia WGS AF: 0.0580 AC: 202 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.7
DANN	Benign	0.42
PhyloP100		0.94

Splicing

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

Other links and lift over

dbSNP: rs10518309; hg19: chr4-119990442;