rs10427094

Variant names:

• chr19-50919621-C-T
• rs10427094

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 0.0945 in 152,208 control chromosomes in the GnomAD database, including 1,054 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 0.094 (1054 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.04
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 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: 0.0943 AC: 14348 AN: 152090 Hom.: 1051 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0857

Gnomad ASJ AF: 0.0153

Gnomad EAS AF: 0.0852

Gnomad SAS AF: 0.0462

Gnomad FIN AF: 0.0657

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0468

Gnomad OTH AF: 0.0747

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

GnomAD4 genome AF: 0.0945 AC: 14377 AN: 152208 Hom.: 1054 Cov.: 32 AF XY: 0.0955 AC XY: 7106 AN XY: 74412

African (AFR) AF: 0.200 AC: 8292 AN: 41522

American (AMR) AF: 0.0858 AC: 1311 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0153 AC: 53 AN: 3472

East Asian (EAS) AF: 0.0856 AC: 443 AN: 5176

South Asian (SAS) AF: 0.0461 AC: 222 AN: 4818

European-Finnish (FIN) AF: 0.0657 AC: 697 AN: 10606

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0468 AC: 3185 AN: 68010

Other (OTH) AF: 0.0744 AC: 157 AN: 2110

Alfa AF: 0.0571 Hom.: 744

Bravo AF: 0.101

Asia WGS AF: 0.0650 AC: 226 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	0.82
DANN	Benign	0.57
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs10427094; hg19: chr19-51422877;