rs2475377

Variant names:

• chr10-94930614-C-T
• rs2475377

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 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

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;