rs7046385

Variant names:

• chr9-103841952-T-C
• rs7046385

Your query was ambiguous. Multiple possible variants found:

• chr9-103841952-T-C
• chr9-103841952-T-G

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 0.351 in 151,916 control chromosomes in the GnomAD database, including 9,504 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 0.35 (9504 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.363 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: 0.351 AC: 53238 AN: 151798 Hom.: 9503 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.351 AC: 53254 AN: 151916 Hom.: 9504 Cov.: 32 AF XY: 0.354 AC XY: 26311 AN XY: 74238

African (AFR) AF: 0.322 AC: 13326 AN: 41420

American (AMR) AF: 0.299 AC: 4558 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1018 AN: 3466

East Asian (EAS) AF: 0.368 AC: 1899 AN: 5158

South Asian (SAS) AF: 0.326 AC: 1573 AN: 4822

European-Finnish (FIN) AF: 0.479 AC: 5054 AN: 10546

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.367 AC: 24896 AN: 67928

Other (OTH) AF: 0.312 AC: 659 AN: 2110

Alfa AF: 0.352 Hom.: 30152

Bravo AF: 0.337

Asia WGS AF: 0.344 AC: 1197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.72
DANN	Benign	0.65
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs7046385; hg19: chr9-106604233;