10-27503160-A-G

Variant names:

• chr10-27503160-A-G
• rs10764698

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 0.503 in 151,980 control chromosomes in the GnomAD database, including 19,288 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 0.50 (19288 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.503 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: 0.503 AC: 76354 AN: 151862 Hom.: 19285 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.503 AC: 76388 AN: 151980 Hom.: 19288 Cov.: 32 AF XY: 0.503 AC XY: 37363 AN XY: 74276

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.590

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.520

Gnomad4 FIN AF: 0.531

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.478

Alfa AF: 0.505 Hom.: 18730

Bravo AF: 0.493

Asia WGS AF: 0.477 AC: 1656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.4
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10764698; hg19: chr10-27792089;