rs7853377

Variant names:

• chr9-83937290-A-G
• rs7853377

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 0.238 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
• Publications: 35 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.333 AC: 13756 AN: 41338

American (AMR) AF: 0.171 AC: 2607 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 706 AN: 3466

East Asian (EAS) AF: 0.00136 AC: 7 AN: 5158

South Asian (SAS) AF: 0.208 AC: 994 AN: 4786

European-Finnish (FIN) AF: 0.210 AC: 2201 AN: 10498

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15112 AN: 67954

Other (OTH) AF: 0.237 AC: 500 AN: 2106

Alfa AF: 0.0254 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
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs7853377; hg19: chr9-86552205;