rs656455

Variant names:

• chr10-35754051-G-A
• rs656455

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 0.225 in 152,112 control chromosomes in the GnomAD database, including 4,705 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 0.22 (4705 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.787
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.329 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: 0.225 AC: 34214 AN: 151994 Hom.: 4706 Cov.: 32

Gnomad AFR AF: 0.0564

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.225 AC: 34203 AN: 152112 Hom.: 4705 Cov.: 32 AF XY: 0.226 AC XY: 16835 AN XY: 74348

African (AFR) AF: 0.0562 AC: 2336 AN: 41532

American (AMR) AF: 0.265 AC: 4054 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 992 AN: 3466

East Asian (EAS) AF: 0.337 AC: 1736 AN: 5146

South Asian (SAS) AF: 0.343 AC: 1651 AN: 4816

European-Finnish (FIN) AF: 0.258 AC: 2728 AN: 10560

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.290 AC: 19713 AN: 67986

Other (OTH) AF: 0.249 AC: 526 AN: 2116

Alfa AF: 0.254 Hom.: 653

Bravo AF: 0.219

Asia WGS AF: 0.270 AC: 939 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	2.0
DANN	Benign	0.88
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs656455; hg19: chr10-36042979;