rs7039300

Variant names:

• chr9-14064742-T-G
• rs7039300

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 0.231 in 152,128 control chromosomes in the GnomAD database, including 4,269 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 (4269 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.348
• Publications: 5 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 (SAS) allele frequency at 95% confidence interval = 0.411 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: 0.231 AC: 35144 AN: 152010 Hom.: 4265 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.231 AC: 35169 AN: 152128 Hom.: 4269 Cov.: 32 AF XY: 0.236 AC XY: 17516 AN XY: 74356

African (AFR) AF: 0.210 AC: 8702 AN: 41524

American (AMR) AF: 0.313 AC: 4768 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 971 AN: 3472

East Asian (EAS) AF: 0.264 AC: 1360 AN: 5152

South Asian (SAS) AF: 0.426 AC: 2055 AN: 4822

European-Finnish (FIN) AF: 0.190 AC: 2012 AN: 10594

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14463 AN: 67998

Other (OTH) AF: 0.260 AC: 549 AN: 2110

Alfa AF: 0.226 Hom.: 11404

Bravo AF: 0.237

Asia WGS AF: 0.334 AC: 1161 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	1.8
DANN	Benign	0.74
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs7039300; hg19: chr9-14064741;