chr7-9499649-C-T

Variant names:

• chr7-9499649-C-T
• rs9918508

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 0.083 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.117 AC: 4866 AN: 41508

American (AMR) AF: 0.0546 AC: 834 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0579 AC: 201 AN: 3472

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5180

South Asian (SAS) AF: 0.0674 AC: 325 AN: 4824

European-Finnish (FIN) AF: 0.0348 AC: 368 AN: 10574

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0843 AC: 5733 AN: 67988

Other (OTH) AF: 0.0799 AC: 169 AN: 2114

Alfa AF: 0.0834 Hom.: 1785

Bravo AF: 0.0849

Asia WGS AF: 0.0480 AC: 169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.7
DANN	Benign	0.46
PhyloP100		-0.12

Splicing

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

Other links and lift over

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