10-72018509-C-T

Variant names:

• chr10-72018509-C-T
• rs1245582

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 0.66 in 152,086 control chromosomes in the GnomAD database, including 34,683 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 0.66 (34683 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.874 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: 0.660 AC: 100330 AN: 151968 Hom.: 34634 Cov.: 32

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.660 AC: 100433 AN: 152086 Hom.: 34683 Cov.: 32 AF XY: 0.650 AC XY: 48332 AN XY: 74334

African (AFR) AF: 0.882 AC: 36613 AN: 41514

American (AMR) AF: 0.616 AC: 9414 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1705 AN: 3470

East Asian (EAS) AF: 0.412 AC: 2129 AN: 5168

South Asian (SAS) AF: 0.508 AC: 2449 AN: 4820

European-Finnish (FIN) AF: 0.535 AC: 5647 AN: 10558

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.595 AC: 40432 AN: 67946

Other (OTH) AF: 0.647 AC: 1366 AN: 2110

Alfa AF: 0.615 Hom.: 93921

Bravo AF: 0.677

Asia WGS AF: 0.507 AC: 1765 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.80
DANN	Benign	0.45
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs1245582; hg19: chr10-73778267;