chr10-44686868-A-G

Variant names:

• chr10-44686868-A-G
• rs999473

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 0.375 in 152,064 control chromosomes in the GnomAD database, including 12,743 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 0.38 (12743 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.614 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: 0.375 AC: 57008 AN: 151946 Hom.: 12708 Cov.: 32

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.375 AC: 57089 AN: 152064 Hom.: 12743 Cov.: 32 AF XY: 0.369 AC XY: 27424 AN XY: 74342

African (AFR) AF: 0.620 AC: 25700 AN: 41448

American (AMR) AF: 0.253 AC: 3864 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 973 AN: 3468

East Asian (EAS) AF: 0.498 AC: 2575 AN: 5166

South Asian (SAS) AF: 0.251 AC: 1210 AN: 4816

European-Finnish (FIN) AF: 0.234 AC: 2473 AN: 10584

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19179 AN: 67978

Other (OTH) AF: 0.342 AC: 724 AN: 2114

Alfa AF: 0.309 Hom.: 27079

Bravo AF: 0.391

Asia WGS AF: 0.385 AC: 1337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.48
PhyloP100		0.028

Splicing

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

Other links and lift over

dbSNP: rs999473; hg19: chr10-45182316;