rs2154175

Variant names:

• chr10-127627260-G-T
• rs2154175

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;