rs7038415

Variant names:

• chr9-110354903-C-A
• rs7038415

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 0.19 in 151,866 control chromosomes in the GnomAD database, including 2,817 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 0.19 (2817 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.238 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: 0.190 AC: 28822 AN: 151748 Hom.: 2811 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0555

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.190 AC: 28847 AN: 151866 Hom.: 2817 Cov.: 32 AF XY: 0.192 AC XY: 14220 AN XY: 74194

African (AFR) AF: 0.242 AC: 10023 AN: 41418

American (AMR) AF: 0.184 AC: 2809 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 511 AN: 3466

East Asian (EAS) AF: 0.0553 AC: 286 AN: 5176

South Asian (SAS) AF: 0.138 AC: 661 AN: 4802

European-Finnish (FIN) AF: 0.241 AC: 2529 AN: 10506

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11443 AN: 67924

Other (OTH) AF: 0.168 AC: 354 AN: 2108

Alfa AF: 0.309 Hom.: 11247

Bravo AF: 0.314

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.45
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs7038415; hg19: chr9-113117183;