1-189754493-A-G

Variant names:

• chr1-189754493-A-G
• rs10737562

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.552 in 152,032 control chromosomes in the GnomAD database, including 24,307 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 0.55 (24307 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.797

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.726 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: 0.552 AC: 83917 AN: 151916 Hom.: 24284 Cov.: 32

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.552 AC: 83984 AN: 152032 Hom.: 24307 Cov.: 32 AF XY: 0.547 AC XY: 40666 AN XY: 74316

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.489

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.527

Gnomad4 NFE AF: 0.495

Gnomad4 OTH AF: 0.515

Alfa AF: 0.494 Hom.: 18205

Bravo AF: 0.558

Asia WGS AF: 0.440 AC: 1532 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10737562; hg19: chr1-189723623;