rs2154175

chr10-127627260-G-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 0.381 in 151,978 control chromosomes in the GnomAD database, including 11,507 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 0.38 (11507 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.462

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.382 AC: 57956 AN: 151860 Hom.: 11502 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.0620

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.381 AC: 57978 AN: 151978 Hom.: 11507 Cov.: 32 AF XY: 0.375 AC XY: 27883 AN XY: 74312

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.0621

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.365

Alfa AF: 0.410 Hom.: 6149

Bravo AF: 0.373

Asia WGS AF: 0.178 AC: 621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	10
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2154175; hg19: chr10-129425524;