rs10748709

Variant names:

• chr10-97777733-G-A
• rs10748709

Your query was ambiguous. Multiple possible variants found:

• chr10-97777733-G-A
• chr10-97777733-G-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 0.837 in 152,096 control chromosomes in the GnomAD database, including 54,141 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 0.84 (54141 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.955 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: 0.837 AC: 127254 AN: 151978 Hom.: 54089 Cov.: 30

Gnomad AFR AF: 0.963

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.816

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.863

Gnomad NFE AF: 0.820

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.837 AC: 127353 AN: 152096 Hom.: 54141 Cov.: 30 AF XY: 0.832 AC XY: 61912 AN XY: 74370

Gnomad4 AFR AF: 0.963

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.816

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.787

Gnomad4 FIN AF: 0.831

Gnomad4 NFE AF: 0.820

Gnomad4 OTH AF: 0.816

Alfa AF: 0.815 Hom.: 92471

Bravo AF: 0.829

Asia WGS AF: 0.701 AC: 2439 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	1.3
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10748709; hg19: chr10-99537490;