10-44608967-G-T

Variant names:

• chr10-44608967-G-T
• rs7069381

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 0.456 in 151,994 control chromosomes in the GnomAD database, including 16,142 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 0.46 (16142 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.392
• Publications: 2 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 (SAS) allele frequency at 95% confidence interval = 0.519 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: 0.456 AC: 69241 AN: 151876 Hom.: 16124 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.456 AC: 69312 AN: 151994 Hom.: 16142 Cov.: 32 AF XY: 0.460 AC XY: 34180 AN XY: 74316

African (AFR) AF: 0.369 AC: 15318 AN: 41456

American (AMR) AF: 0.504 AC: 7699 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1373 AN: 3470

East Asian (EAS) AF: 0.523 AC: 2699 AN: 5156

South Asian (SAS) AF: 0.536 AC: 2577 AN: 4810

European-Finnish (FIN) AF: 0.529 AC: 5583 AN: 10556

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.478 AC: 32461 AN: 67958

Other (OTH) AF: 0.457 AC: 965 AN: 2110

Alfa AF: 0.372 Hom.: 1463

Bravo AF: 0.454

Asia WGS AF: 0.543 AC: 1891 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	2.6
DANN	Benign	0.67
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs7069381; hg19: chr10-45104415;