rs1372189

Variant names:

• chr10-107541487-C-T
• rs1372189

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 0.311 in 151,814 control chromosomes in the GnomAD database, including 9,077 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 0.31 (9077 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.08
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.447 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: 0.311 AC: 47193 AN: 151696 Hom.: 9071 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.0514

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.311 AC: 47207 AN: 151814 Hom.: 9077 Cov.: 32 AF XY: 0.302 AC XY: 22417 AN XY: 74206

African (AFR) AF: 0.112 AC: 4666 AN: 41488

American (AMR) AF: 0.280 AC: 4262 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1382 AN: 3466

East Asian (EAS) AF: 0.0512 AC: 265 AN: 5180

South Asian (SAS) AF: 0.249 AC: 1204 AN: 4826

European-Finnish (FIN) AF: 0.356 AC: 3748 AN: 10532

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.451 AC: 30593 AN: 67782

Other (OTH) AF: 0.300 AC: 633 AN: 2110

Alfa AF: 0.362 Hom.: 1970

Bravo AF: 0.297

Asia WGS AF: 0.154 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.026
DANN	Benign	0.48
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs1372189; hg19: chr10-109301245;