chr9-99077591-A-G

Variant names:

• chr9-99077591-A-G
• rs4742761

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 0.312 in 152,148 control chromosomes in the GnomAD database, including 8,608 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 0.31 (8608 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.649 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: 0.312 AC: 47464 AN: 152030 Hom.: 8583 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.312 AC: 47527 AN: 152148 Hom.: 8608 Cov.: 32 AF XY: 0.316 AC XY: 23534 AN XY: 74408

African (AFR) AF: 0.420 AC: 17416 AN: 41492

American (AMR) AF: 0.332 AC: 5071 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 782 AN: 3470

East Asian (EAS) AF: 0.667 AC: 3457 AN: 5180

South Asian (SAS) AF: 0.568 AC: 2739 AN: 4820

European-Finnish (FIN) AF: 0.170 AC: 1798 AN: 10592

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15302 AN: 67994

Other (OTH) AF: 0.334 AC: 704 AN: 2110

Alfa AF: 0.264 Hom.: 792

Bravo AF: 0.326

Asia WGS AF: 0.633 AC: 2201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.58
DANN	Benign	0.58
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4742761; hg19: chr9-101839873;