chr10-56169007-C-T

Variant names:

• chr10-56169007-C-T
• rs11005240

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 0.033 in 151,614 control chromosomes in the GnomAD database, including 104 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 0.033 (104 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.106 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: 0.0331 AC: 5020 AN: 151496 Hom.: 104 Cov.: 32

Gnomad AFR AF: 0.0165

Gnomad AMI AF: 0.00440

Gnomad AMR AF: 0.0351

Gnomad ASJ AF: 0.0779

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.0795

Gnomad FIN AF: 0.0391

Gnomad MID AF: 0.0764

Gnomad NFE AF: 0.0299

Gnomad OTH AF: 0.0451

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

GnomAD4 genome AF: 0.0330 AC: 5010 AN: 151614 Hom.: 104 Cov.: 32 AF XY: 0.0351 AC XY: 2602 AN XY: 74124

African (AFR) AF: 0.0165 AC: 675 AN: 41002

American (AMR) AF: 0.0349 AC: 532 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.0779 AC: 270 AN: 3468

East Asian (EAS) AF: 0.113 AC: 587 AN: 5172

South Asian (SAS) AF: 0.0792 AC: 382 AN: 4826

European-Finnish (FIN) AF: 0.0391 AC: 414 AN: 10592

Middle Eastern (MID) AF: 0.0651 AC: 19 AN: 292

European-Non Finnish (NFE) AF: 0.0299 AC: 2033 AN: 68008

Other (OTH) AF: 0.0447 AC: 94 AN: 2104

Alfa AF: 0.0345 Hom.: 56

Bravo AF: 0.0332

Asia WGS AF: 0.0730 AC: 251 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.94
DANN	Benign	0.31
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs11005240; hg19: chr10-57928768;