rs7874443

Variant names:

• chr9-86110841-T-C
• rs7874443

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 0.687 in 152,074 control chromosomes in the GnomAD database, including 37,243 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 0.69 (37243 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

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 = 0.795 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: 0.687 AC: 104392 AN: 151956 Hom.: 37211 Cov.: 33

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.687 AC: 104479 AN: 152074 Hom.: 37243 Cov.: 33 AF XY: 0.674 AC XY: 50087 AN XY: 74340

Gnomad4 AFR AF: 0.802

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.663

Gnomad4 NFE AF: 0.704

Gnomad4 OTH AF: 0.647

Alfa AF: 0.673 Hom.: 24887

Bravo AF: 0.687

Asia WGS AF: 0.307 AC: 1070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.53
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7874443; hg19: chr9-88725756;