9-96234971-G-C

Variant names:

• chr9-96234971-G-C
• rs1324196

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 0.485 in 151,954 control chromosomes in the GnomAD database, including 18,315 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 0.48 (18315 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.340

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.561 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: 0.485 AC: 73606 AN: 151836 Hom.: 18301 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.485 AC: 73654 AN: 151954 Hom.: 18315 Cov.: 32 AF XY: 0.489 AC XY: 36357 AN XY: 74286

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.571

Gnomad4 ASJ AF: 0.422

Gnomad4 EAS AF: 0.568

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.482

Alfa AF: 0.393 Hom.: 1198

Bravo AF: 0.481

Asia WGS AF: 0.534 AC: 1856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.8
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1324196; hg19: chr9-98997253;