10-44715242-T-G

Variant names:

• chr10-44715242-T-G
• rs7097094

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 0.365 in 151,888 control chromosomes in the GnomAD database, including 11,699 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 0.36 (11699 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.382
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.577 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: 0.364 AC: 55301 AN: 151770 Hom.: 11662 Cov.: 32

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.365 AC: 55386 AN: 151888 Hom.: 11699 Cov.: 32 AF XY: 0.359 AC XY: 26633 AN XY: 74242

African (AFR) AF: 0.583 AC: 24134 AN: 41368

American (AMR) AF: 0.248 AC: 3785 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 967 AN: 3466

East Asian (EAS) AF: 0.451 AC: 2313 AN: 5134

South Asian (SAS) AF: 0.263 AC: 1263 AN: 4798

European-Finnish (FIN) AF: 0.235 AC: 2486 AN: 10572

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19339 AN: 67950

Other (OTH) AF: 0.336 AC: 707 AN: 2106

Alfa AF: 0.281 Hom.: 3809

Bravo AF: 0.378

Asia WGS AF: 0.366 AC: 1273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	10
DANN	Benign	0.53
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs7097094; hg19: chr10-45210690;