rs10508755

Variant names:

• chr10-29957351-G-A
• rs10508755

Your query was ambiguous. Multiple possible variants found:

• chr10-29957351-G-A
• chr10-29957351-G-T

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 0.107 in 152,068 control chromosomes in the GnomAD database, including 2,554 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 0.11 (2554 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 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: 0.106 AC: 16172 AN: 151950 Hom.: 2537 Cov.: 33

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0442

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.0688

Gnomad FIN AF: 0.000850

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.00847

Gnomad OTH AF: 0.0845

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

GnomAD4 genome AF: 0.107 AC: 16227 AN: 152068 Hom.: 2554 Cov.: 33 AF XY: 0.104 AC XY: 7766 AN XY: 74322

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.0443

Gnomad4 ASJ AF: 0.0297

Gnomad4 EAS AF: 0.00271

Gnomad4 SAS AF: 0.0680

Gnomad4 FIN AF: 0.000850

Gnomad4 NFE AF: 0.00848

Gnomad4 OTH AF: 0.0837

Alfa AF: 0.0168 Hom.: 39

Bravo AF: 0.120

Asia WGS AF: 0.0480 AC: 167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.98
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10508755; hg19: chr10-30246280;