10-23376509-G-T

Variant names:

• chr10-23376509-G-T
• rs1398024

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 0.303 in 152,064 control chromosomes in the GnomAD database, including 8,314 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 0.30 (8314 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.904
• Publications: 28 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.483 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: 0.302 AC: 45958 AN: 151946 Hom.: 8289 Cov.: 32

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.0830

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.303 AC: 46031 AN: 152064 Hom.: 8314 Cov.: 32 AF XY: 0.300 AC XY: 22284 AN XY: 74344

African (AFR) AF: 0.489 AC: 20273 AN: 41460

American (AMR) AF: 0.371 AC: 5663 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1166 AN: 3470

East Asian (EAS) AF: 0.0832 AC: 431 AN: 5182

South Asian (SAS) AF: 0.220 AC: 1060 AN: 4826

European-Finnish (FIN) AF: 0.189 AC: 2000 AN: 10590

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.213 AC: 14489 AN: 67958

Other (OTH) AF: 0.313 AC: 660 AN: 2108

Alfa AF: 0.247 Hom.: 22414

Bravo AF: 0.327

Asia WGS AF: 0.184 AC: 644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.6
DANN	Benign	0.75
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs1398024; hg19: chr10-23665438;