rs9648058

Variant names:

• chr7-38070256-C-A
• rs9648058

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 0.0577 in 152,144 control chromosomes in the GnomAD database, including 346 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 0.058 (346 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.457
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.128 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: 0.0577 AC: 8772 AN: 152026 Hom.: 345 Cov.: 32

Gnomad AFR AF: 0.0123

Gnomad AMI AF: 0.0956

Gnomad AMR AF: 0.0592

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.0485

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0731

Gnomad OTH AF: 0.0730

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

GnomAD4 genome AF: 0.0577 AC: 8774 AN: 152144 Hom.: 346 Cov.: 32 AF XY: 0.0593 AC XY: 4409 AN XY: 74372

African (AFR) AF: 0.0123 AC: 509 AN: 41510

American (AMR) AF: 0.0592 AC: 905 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 389 AN: 3470

East Asian (EAS) AF: 0.106 AC: 551 AN: 5180

South Asian (SAS) AF: 0.137 AC: 659 AN: 4812

European-Finnish (FIN) AF: 0.0485 AC: 513 AN: 10572

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0731 AC: 4973 AN: 67994

Other (OTH) AF: 0.0727 AC: 153 AN: 2104

Alfa AF: 0.0656 Hom.: 65

Bravo AF: 0.0543

Asia WGS AF: 0.0990 AC: 345 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	4.1
DANN	Benign	0.74
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs9648058; hg19: chr7-38109858;