rs7849014

chr9-136563054-C-T

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 0.867 in 152,256 control chromosomes in the GnomAD database, including 57,761 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 0.87 (57761 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.713

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.867 AC: 131924 AN: 152138 Hom.: 57746 Cov.: 34

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.919

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 0.909

Gnomad SAS AF: 0.876

Gnomad FIN AF: 0.950

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.918

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.867 AC: 131988 AN: 152256 Hom.: 57761 Cov.: 34 AF XY: 0.871 AC XY: 64887 AN XY: 74468

Gnomad4 AFR AF: 0.731

Gnomad4 AMR AF: 0.919

Gnomad4 ASJ AF: 0.921

Gnomad4 EAS AF: 0.909

Gnomad4 SAS AF: 0.876

Gnomad4 FIN AF: 0.950

Gnomad4 NFE AF: 0.918

Gnomad4 OTH AF: 0.875

Alfa AF: 0.910 Hom.: 100537

Bravo AF: 0.860

Asia WGS AF: 0.876 AC: 3046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	3.5
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7849014; hg19: chr9-139457506;