rs10102546

Variant names:

• chr8-119544334-C-T
• rs10102546

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.543 in 152,096 control chromosomes in the GnomAD database, including 23,848 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 0.54 (23848 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.893
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.739 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: 0.543 AC: 82500 AN: 151978 Hom.: 23810 Cov.: 32

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.543 AC: 82599 AN: 152096 Hom.: 23848 Cov.: 32 AF XY: 0.545 AC XY: 40496 AN XY: 74364

African (AFR) AF: 0.746 AC: 30949 AN: 41494

American (AMR) AF: 0.540 AC: 8250 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1604 AN: 3468

East Asian (EAS) AF: 0.337 AC: 1746 AN: 5178

South Asian (SAS) AF: 0.587 AC: 2832 AN: 4822

European-Finnish (FIN) AF: 0.518 AC: 5476 AN: 10568

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 30072 AN: 67978

Other (OTH) AF: 0.505 AC: 1066 AN: 2110

Alfa AF: 0.492 Hom.: 11243

Bravo AF: 0.547

Asia WGS AF: 0.518 AC: 1800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.24
DANN	Benign	0.49
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs10102546; hg19: chr8-120556574;