rs10509955

Variant names:

• chr10-111994277-C-T
• rs10509955

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 0.311 in 149,196 control chromosomes in the GnomAD database, including 9,059 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 0.31 (9059 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.548 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: 0.311 AC: 46346 AN: 149080 Hom.: 9038 Cov.: 33

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.311 AC: 46410 AN: 149196 Hom.: 9059 Cov.: 33 AF XY: 0.316 AC XY: 23050 AN XY: 72998

African (AFR) AF: 0.554 AC: 21435 AN: 38704

American (AMR) AF: 0.426 AC: 6464 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1058 AN: 3472

East Asian (EAS) AF: 0.401 AC: 2073 AN: 5170

South Asian (SAS) AF: 0.345 AC: 1664 AN: 4824

European-Finnish (FIN) AF: 0.140 AC: 1488 AN: 10600

Middle Eastern (MID) AF: 0.253 AC: 74 AN: 292

European-Non Finnish (NFE) AF: 0.169 AC: 11465 AN: 67970

Other (OTH) AF: 0.302 AC: 625 AN: 2068

Alfa AF: 0.247 Hom.: 2600

Bravo AF: 0.337

Asia WGS AF: 0.376 AC: 1308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.7
DANN	Benign	0.70
PhyloP100		-0.059

Splicing

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

Other links and lift over

dbSNP: rs10509955; hg19: chr10-113754035;