rs7853377

Variant names:

• chr9-83937290-A-G
• rs7853377

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 0.238 in 151,746 control chromosomes in the GnomAD database, including 4,779 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 0.24 (4779 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.328 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: 0.238 AC: 36092 AN: 151628 Hom.: 4782 Cov.: 31

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.238 AC: 36101 AN: 151746 Hom.: 4779 Cov.: 31 AF XY: 0.237 AC XY: 17561 AN XY: 74168

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.00136

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.237

Alfa AF: 0.0331 Hom.: 576

Bravo AF: 0.237

Asia WGS AF: 0.0990 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7853377; hg19: chr9-86552205;