rs6588761

Positions:

• chr10-47139553-G-A

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 0.0848 in 151,968 control chromosomes in the GnomAD database, including 1,255 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 0.085 (1255 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.990

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0846 AC: 12850 AN: 151850 Hom.: 1251 Cov.: 30

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0542

Gnomad ASJ AF: 0.0985

Gnomad EAS AF: 0.000966

Gnomad SAS AF: 0.0120

Gnomad FIN AF: 0.00547

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0222

Gnomad OTH AF: 0.0844

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

GnomAD4 genome AF: 0.0848 AC: 12880 AN: 151968 Hom.: 1255 Cov.: 30 AF XY: 0.0814 AC XY: 6049 AN XY: 74298

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.0540

Gnomad4 ASJ AF: 0.0985

Gnomad4 EAS AF: 0.000968

Gnomad4 SAS AF: 0.0123

Gnomad4 FIN AF: 0.00547

Gnomad4 NFE AF: 0.0222

Gnomad4 OTH AF: 0.0835

Alfa AF: 0.0596 Hom.: 101

Bravo AF: 0.0965

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6588761; hg19: chr10-48599809;