rs9918508

Variant names:

• chr7-9499649-C-T
• rs9918508

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 0.083 in 152,152 control chromosomes in the GnomAD database, including 599 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 0.083 (599 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.114 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: 0.0830 AC: 12617 AN: 152034 Hom.: 597 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0547

Gnomad ASJ AF: 0.0579

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0659

Gnomad FIN AF: 0.0348

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0843

Gnomad OTH AF: 0.0808

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

GnomAD4 genome AF: 0.0830 AC: 12626 AN: 152152 Hom.: 599 Cov.: 32 AF XY: 0.0792 AC XY: 5888 AN XY: 74390

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.0546

Gnomad4 ASJ AF: 0.0579

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0674

Gnomad4 FIN AF: 0.0348

Gnomad4 NFE AF: 0.0843

Gnomad4 OTH AF: 0.0799

Alfa AF: 0.0821 Hom.: 1157

Bravo AF: 0.0849

Asia WGS AF: 0.0480 AC: 169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.7
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9918508; hg19: chr7-9539279; COSMIC: COSV60007867;