rs9691864

Positions:

• chr7-54824378-G-A

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 0.302 in 151,736 control chromosomes in the GnomAD database, including 7,583 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 0.30 (7583 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.789

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.54824378G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45762 AN: 151618 Hom.: 7589 Cov.: 31

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.0738

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.302 AC: 45764 AN: 151736 Hom.: 7583 Cov.: 31 AF XY: 0.295 AC XY: 21879 AN XY: 74148

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.0739

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.327

Alfa AF: 0.368 Hom.: 13574

Bravo AF: 0.299

Asia WGS AF: 0.182 AC: 632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	4.0
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9691864; hg19: chr7-54892071;