chr9-7393934-T-C

Variant names:

• chr9-7393934-T-C
• rs7033457

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 0.282 in 152,128 control chromosomes in the GnomAD database, including 6,955 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 0.28 (6955 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.452
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.437 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: 0.281 AC: 42773 AN: 152010 Hom.: 6932 Cov.: 33

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.282 AC: 42832 AN: 152128 Hom.: 6955 Cov.: 33 AF XY: 0.276 AC XY: 20541 AN XY: 74388

African (AFR) AF: 0.443 AC: 18351 AN: 41458

American (AMR) AF: 0.221 AC: 3380 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 788 AN: 3468

East Asian (EAS) AF: 0.285 AC: 1476 AN: 5172

South Asian (SAS) AF: 0.372 AC: 1796 AN: 4824

European-Finnish (FIN) AF: 0.137 AC: 1448 AN: 10594

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14691 AN: 68002

Other (OTH) AF: 0.269 AC: 569 AN: 2114

Alfa AF: 0.238 Hom.: 19728

Bravo AF: 0.293

Asia WGS AF: 0.361 AC: 1254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	9.5
DANN	Benign	0.65
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs7033457; hg19: chr9-7393934; COSMIC: COSV69444841;