rs2127355

Variant names:

• chr10-60774458-A-G
• rs2127355

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 0.51 in 152,058 control chromosomes in the GnomAD database, including 20,085 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 0.51 (20085 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.823
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.681 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: 0.510 AC: 77491 AN: 151940 Hom.: 20055 Cov.: 32

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.510 AC: 77578 AN: 152058 Hom.: 20085 Cov.: 32 AF XY: 0.512 AC XY: 38049 AN XY: 74326

African (AFR) AF: 0.551 AC: 22836 AN: 41440

American (AMR) AF: 0.549 AC: 8393 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1421 AN: 3472

East Asian (EAS) AF: 0.700 AC: 3617 AN: 5166

South Asian (SAS) AF: 0.512 AC: 2465 AN: 4816

European-Finnish (FIN) AF: 0.522 AC: 5517 AN: 10570

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.468 AC: 31784 AN: 67984

Other (OTH) AF: 0.483 AC: 1021 AN: 2114

Alfa AF: 0.490 Hom.: 19042

Bravo AF: 0.520

Asia WGS AF: 0.583 AC: 2028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.60
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs2127355; hg19: chr10-62534216;