rs7042508

chr9-38746454-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0958 in 152,026 control chromosomes in the GnomAD database, including 1,023 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 0.096 (1023 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.105

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0957 AC: 14542 AN: 151906 Hom.: 1019 Cov.: 33

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0561

Gnomad ASJ AF: 0.0813

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.0236

Gnomad FIN AF: 0.0422

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0622

Gnomad OTH AF: 0.0815

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

GnomAD4 genome AF: 0.0958 AC: 14568 AN: 152026 Hom.: 1023 Cov.: 33 AF XY: 0.0926 AC XY: 6884 AN XY: 74340

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.0560

Gnomad4 ASJ AF: 0.0813

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.0240

Gnomad4 FIN AF: 0.0422

Gnomad4 NFE AF: 0.0622

Gnomad4 OTH AF: 0.0797

Alfa AF: 0.0768 Hom.: 72

Bravo AF: 0.104

Asia WGS AF: 0.0560 AC: 194 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	1.0
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7042508; hg19: chr9-38746451;