rs2475377

Positions:

• chr10-94930614-C-T

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 0.0587 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.0574

Gnomad4 ASJ AF: 0.0681

Gnomad4 EAS AF: 0.0244

Gnomad4 SAS AF: 0.0214

Gnomad4 FIN AF: 0.0305

Gnomad4 NFE AF: 0.0427

Gnomad4 OTH AF: 0.0627

Alfa AF: 0.0487 Hom.: 274

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2475377; hg19: chr10-96690371;