rs10244364

Variant names:

• chr7-117889587-T-C
• rs10244364

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 0.285 in 152,156 control chromosomes in the GnomAD database, including 6,794 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 0.28 (6794 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.334
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.348 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: 0.285 AC: 43310 AN: 152038 Hom.: 6790 Cov.: 33

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.285 AC: 43329 AN: 152156 Hom.: 6794 Cov.: 33 AF XY: 0.292 AC XY: 21698 AN XY: 74384

African (AFR) AF: 0.196 AC: 8135 AN: 41534

American (AMR) AF: 0.215 AC: 3279 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 788 AN: 3468

East Asian (EAS) AF: 0.172 AC: 891 AN: 5166

South Asian (SAS) AF: 0.362 AC: 1745 AN: 4822

European-Finnish (FIN) AF: 0.462 AC: 4882 AN: 10570

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22879 AN: 67998

Other (OTH) AF: 0.252 AC: 532 AN: 2114

Alfa AF: 0.324 Hom.: 1108

Bravo AF: 0.255

Asia WGS AF: 0.242 AC: 844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.7
DANN	Benign	0.78
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs10244364; hg19: chr7-117529641;