rs10078761

Variant names:

• chr5-1249479-T-A
• rs10078761

Your query was ambiguous. Multiple possible variants found:

• chr5-1249479-T-A
• chr5-1249479-T-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 0.309 in 152,034 control chromosomes in the GnomAD database, including 7,585 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 0.31 (7585 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47029 AN: 151916 Hom.: 7585 Cov.: 33

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.0372

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.309 AC: 47044 AN: 152034 Hom.: 7585 Cov.: 33 AF XY: 0.306 AC XY: 22715 AN XY: 74348

African (AFR) AF: 0.286 AC: 11836 AN: 41454

American (AMR) AF: 0.275 AC: 4210 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1423 AN: 3468

East Asian (EAS) AF: 0.0369 AC: 191 AN: 5170

South Asian (SAS) AF: 0.274 AC: 1321 AN: 4820

European-Finnish (FIN) AF: 0.341 AC: 3612 AN: 10590

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.342 AC: 23259 AN: 67932

Other (OTH) AF: 0.343 AC: 723 AN: 2110

Alfa AF: 0.205 Hom.: 473

Bravo AF: 0.303

Asia WGS AF: 0.158 AC: 551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.084
DANN	Benign	0.070
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10078761; hg19: chr5-1249594; COSMIC: COSV57206450;