rs1962243

Variant names:

• chr9-71560512-A-G
• rs1962243

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 0.0184 in 152,262 control chromosomes in the GnomAD database, including 137 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 0.018 (137 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.71

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.169 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: 0.0184 AC: 2806 AN: 152144 Hom.: 137 Cov.: 32

Gnomad AFR AF: 0.00369

Gnomad AMI AF: 0.0495

Gnomad AMR AF: 0.0481

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.0879

Gnomad FIN AF: 0.0188

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00373

Gnomad OTH AF: 0.0215

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

GnomAD4 genome AF: 0.0184 AC: 2804 AN: 152262 Hom.: 137 Cov.: 32 AF XY: 0.0220 AC XY: 1639 AN XY: 74446

Gnomad4 AFR AF: 0.00370

Gnomad4 AMR AF: 0.0480

Gnomad4 ASJ AF: 0.00490

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.0874

Gnomad4 FIN AF: 0.0188

Gnomad4 NFE AF: 0.00373

Gnomad4 OTH AF: 0.0241

Alfa AF: 0.00927 Hom.: 100

Bravo AF: 0.0200

Asia WGS AF: 0.147 AC: 508 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	9.2
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1962243; hg19: chr9-74175428;