10-55657201-C-T

Variant names:

• chr10-55657201-C-T
• rs1916521

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 0.361 in 151,140 control chromosomes in the GnomAD database, including 9,950 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 0.36 (9950 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.741
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.402 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: 0.361 AC: 54538 AN: 151024 Hom.: 9947 Cov.: 31

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.321

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.361 AC: 54560 AN: 151140 Hom.: 9950 Cov.: 31 AF XY: 0.356 AC XY: 26239 AN XY: 73804

African (AFR) AF: 0.384 AC: 15854 AN: 41272

American (AMR) AF: 0.306 AC: 4649 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1422 AN: 3454

East Asian (EAS) AF: 0.417 AC: 2140 AN: 5132

South Asian (SAS) AF: 0.332 AC: 1595 AN: 4808

European-Finnish (FIN) AF: 0.301 AC: 3156 AN: 10490

Middle Eastern (MID) AF: 0.314 AC: 91 AN: 290

European-Non Finnish (NFE) AF: 0.364 AC: 24576 AN: 67516

Other (OTH) AF: 0.355 AC: 744 AN: 2096

Alfa AF: 0.363 Hom.: 30129

Bravo AF: 0.362

Asia WGS AF: 0.369 AC: 1280 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.3
DANN	Benign	0.74
PhyloP100		0.74

Splicing

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

Other links and lift over

dbSNP: rs1916521; hg19: chr10-57416961;