chr10-94930614-C-T

Variant names:

• chr10-94930614-C-T
• rs2475377

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 0.0587 in 152,128 control chromosomes in the GnomAD database, including 352 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 0.059 (352 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.113
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0983 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: 0.0585 AC: 8895 AN: 152010 Hom.: 346 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0575

Gnomad ASJ AF: 0.0681

Gnomad EAS AF: 0.0243

Gnomad SAS AF: 0.0218

Gnomad FIN AF: 0.0305

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0427

Gnomad OTH AF: 0.0624

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

GnomAD4 genome AF: 0.0587 AC: 8933 AN: 152128 Hom.: 352 Cov.: 32 AF XY: 0.0569 AC XY: 4234 AN XY: 74376

African (AFR) AF: 0.101 AC: 4183 AN: 41488

American (AMR) AF: 0.0574 AC: 876 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0681 AC: 236 AN: 3468

East Asian (EAS) AF: 0.0244 AC: 126 AN: 5172

South Asian (SAS) AF: 0.0214 AC: 103 AN: 4808

European-Finnish (FIN) AF: 0.0305 AC: 324 AN: 10606

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0427 AC: 2907 AN: 68012

Other (OTH) AF: 0.0627 AC: 132 AN: 2106

Alfa AF: 0.0503 Hom.: 373

Bravo AF: 0.0618

Asia WGS AF: 0.0400 AC: 140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.6
DANN	Benign	0.38
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs2475377; hg19: chr10-96690371;