9-91484173-G-A

Variant names:

• chr9-91484173-G-A
• rs4743835

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 0.486 in 152,022 control chromosomes in the GnomAD database, including 22,479 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 0.49 (22479 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73820 AN: 151904 Hom.: 22425 Cov.: 31

Gnomad AFR AF: 0.855

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.486 AC: 73929 AN: 152022 Hom.: 22479 Cov.: 31 AF XY: 0.485 AC XY: 36048 AN XY: 74312

African (AFR) AF: 0.855 AC: 35455 AN: 41474

American (AMR) AF: 0.333 AC: 5090 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1394 AN: 3466

East Asian (EAS) AF: 0.689 AC: 3559 AN: 5166

South Asian (SAS) AF: 0.457 AC: 2201 AN: 4818

European-Finnish (FIN) AF: 0.356 AC: 3761 AN: 10558

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.311 AC: 21106 AN: 67960

Other (OTH) AF: 0.460 AC: 970 AN: 2108

Alfa AF: 0.375 Hom.: 7423

Bravo AF: 0.503

Asia WGS AF: 0.605 AC: 2104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.55
DANN	Benign	0.42
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4743835; hg19: chr9-94246455; COSMIC: COSV60378233;