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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.310 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

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.0369

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.343

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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