9-6335760-A-T

Variant names:

• chr9-6335760-A-T
• rs7850988

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 0.232 in 152,164 control chromosomes in the GnomAD database, including 4,372 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 0.23 (4372 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.258 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: 0.232 AC: 35291 AN: 152046 Hom.: 4371 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.232 AC: 35315 AN: 152164 Hom.: 4372 Cov.: 32 AF XY: 0.230 AC XY: 17086 AN XY: 74388

African (AFR) AF: 0.217 AC: 8998 AN: 41500

American (AMR) AF: 0.201 AC: 3067 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 977 AN: 3466

East Asian (EAS) AF: 0.00173 AC: 9 AN: 5192

South Asian (SAS) AF: 0.186 AC: 896 AN: 4830

European-Finnish (FIN) AF: 0.251 AC: 2656 AN: 10586

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17785 AN: 67984

Other (OTH) AF: 0.247 AC: 523 AN: 2114

Alfa AF: 0.110 Hom.: 174

Bravo AF: 0.230

Asia WGS AF: 0.0850 AC: 299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.59
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs7850988; hg19: chr9-6335760;