rs7874443

Variant names:

• chr9-86110841-T-C
• rs7874443

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 0.687 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.802 AC: 33276 AN: 41504

American (AMR) AF: 0.599 AC: 9146 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2053 AN: 3468

East Asian (EAS) AF: 0.187 AC: 967 AN: 5174

South Asian (SAS) AF: 0.413 AC: 1988 AN: 4814

European-Finnish (FIN) AF: 0.663 AC: 7004 AN: 10558

Middle Eastern (MID) AF: 0.599 AC: 175 AN: 292

European-Non Finnish (NFE) AF: 0.704 AC: 47874 AN: 67968

Other (OTH) AF: 0.647 AC: 1367 AN: 2112

Alfa AF: 0.686 Hom.: 79180

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs7874443; hg19: chr9-88725756;