rs7849014

Variant names:

• chr9-136563054-C-T
• rs7849014

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;