rs1417374

Variant names:

• chr10-22839546-G-A
• rs1417374

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 0.24 in 152,072 control chromosomes in the GnomAD database, including 4,836 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 0.24 (4836 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.683
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.32 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: 0.240 AC: 36488 AN: 151954 Hom.: 4832 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.240 AC: 36490 AN: 152072 Hom.: 4836 Cov.: 32 AF XY: 0.240 AC XY: 17802 AN XY: 74328

African (AFR) AF: 0.133 AC: 5535 AN: 41496

American (AMR) AF: 0.256 AC: 3910 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 900 AN: 3466

East Asian (EAS) AF: 0.168 AC: 872 AN: 5182

South Asian (SAS) AF: 0.333 AC: 1606 AN: 4818

European-Finnish (FIN) AF: 0.265 AC: 2793 AN: 10554

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19978 AN: 67958

Other (OTH) AF: 0.233 AC: 492 AN: 2112

Alfa AF: 0.280 Hom.: 10163

Bravo AF: 0.231

Asia WGS AF: 0.230 AC: 797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.3
DANN	Benign	0.39
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs1417374; hg19: chr10-23128475;