chr7-48846016-T-G

Variant names:

• chr7-48846016-T-G
• rs380962
• ENST00000839179.1:n.317-539T>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000839179.1(ENSG00000309162):​n.317-539T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.75 (32271 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000309162 ENST00000839179.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 2 publications found

Genes affected

ENSG00000309162 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

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
ENSG00000309162	ENST00000839179.1	n.317-539T>G		intron_variant	Intron 2 of 2
ENSG00000309162	ENST00000839180.1	n.284-539T>G		intron_variant	Intron 2 of 2
ENSG00000309162	ENST00000839181.1	n.330-539T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.749 AC: 96596 AN: 128898 Hom.: 32255 Cov.: 33

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.758

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.827

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.781

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.749 AC: 96665 AN: 129004 Hom.: 32271 Cov.: 33 AF XY: 0.748 AC XY: 47168 AN XY: 63018

African (AFR) AF: 0.733 AC: 25891 AN: 35322

American (AMR) AF: 0.744 AC: 9616 AN: 12920

Ashkenazi Jewish (ASJ) AF: 0.799 AC: 2424 AN: 3034

East Asian (EAS) AF: 0.709 AC: 2981 AN: 4204

South Asian (SAS) AF: 0.758 AC: 2964 AN: 3910

European-Finnish (FIN) AF: 0.748 AC: 6570 AN: 8782

Middle Eastern (MID) AF: 0.820 AC: 205 AN: 250

European-Non Finnish (NFE) AF: 0.759 AC: 43994 AN: 57982

Other (OTH) AF: 0.782 AC: 1407 AN: 1800

Alfa AF: 0.801 Hom.: 4923

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.52
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs380962; hg19: chr7-48885612;