rs7042508

Variant names:

• chr9-38746454-G-C
• rs7042508

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;