rs9918553

Positions:

• chr7-38634233-A-G

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 0.32 in 152,120 control chromosomes in the GnomAD database, including 8,563 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 0.32 (8563 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48612 AN: 152002 Hom.: 8539 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.320 AC: 48674 AN: 152120 Hom.: 8563 Cov.: 32 AF XY: 0.325 AC XY: 24163 AN XY: 74376

Gnomad4 AFR AF: 0.455

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.290

Alfa AF: 0.259 Hom.: 7195

Bravo AF: 0.321

Asia WGS AF: 0.382 AC: 1327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9918553; hg19: chr7-38673833;