rs4751759

Variant names:

• chr10-119975030-G-A
• rs4751759

Your query was ambiguous. Multiple possible variants found:

• chr10-119975030-G-A
• chr10-119975030-G-C

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 0.211 in 152,118 control chromosomes in the GnomAD database, including 3,542 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 0.21 (3542 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.248 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: 0.211 AC: 32072 AN: 152000 Hom.: 3536 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.211 AC: 32082 AN: 152118 Hom.: 3542 Cov.: 32 AF XY: 0.214 AC XY: 15887 AN XY: 74362

African (AFR) AF: 0.153 AC: 6362 AN: 41512

American (AMR) AF: 0.228 AC: 3491 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 805 AN: 3468

East Asian (EAS) AF: 0.259 AC: 1341 AN: 5172

South Asian (SAS) AF: 0.139 AC: 672 AN: 4824

European-Finnish (FIN) AF: 0.291 AC: 3070 AN: 10564

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15626 AN: 67976

Other (OTH) AF: 0.216 AC: 456 AN: 2108

Alfa AF: 0.218 Hom.: 6309

Bravo AF: 0.207

Asia WGS AF: 0.169 AC: 588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.59
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4751759; hg19: chr10-121734542;