rs2154175

Variant names:

• chr10-127627260-G-T
• rs2154175

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 0.381 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.386 AC: 15996 AN: 41450

American (AMR) AF: 0.294 AC: 4491 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1341 AN: 3468

East Asian (EAS) AF: 0.0621 AC: 321 AN: 5168

South Asian (SAS) AF: 0.251 AC: 1210 AN: 4824

European-Finnish (FIN) AF: 0.392 AC: 4143 AN: 10582

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29150 AN: 67924

Other (OTH) AF: 0.365 AC: 770 AN: 2108

Alfa AF: 0.411 Hom.: 6840

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
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs2154175; hg19: chr10-129425524;