chr10-80148128-A-T

Variant names:

• chr10-80148128-A-T
• rs2789679

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 0.372 in 152,190 control chromosomes in the GnomAD database, including 11,501 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 0.37 (11501 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.199
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 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: 0.372 AC: 56594 AN: 152072 Hom.: 11502 Cov.: 33

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.372 AC: 56581 AN: 152190 Hom.: 11501 Cov.: 33 AF XY: 0.375 AC XY: 27872 AN XY: 74404

African (AFR) AF: 0.198 AC: 8223 AN: 41532

American (AMR) AF: 0.426 AC: 6514 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1302 AN: 3468

East Asian (EAS) AF: 0.581 AC: 2997 AN: 5162

South Asian (SAS) AF: 0.357 AC: 1719 AN: 4818

European-Finnish (FIN) AF: 0.463 AC: 4903 AN: 10600

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29588 AN: 67994

Other (OTH) AF: 0.394 AC: 831 AN: 2108

Alfa AF: 0.388 Hom.: 1582

Bravo AF: 0.362

Asia WGS AF: 0.421 AC: 1461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.39
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs2789679; hg19: chr10-81907884;