rs7104645

Variant names:

• chr11-2041120-A-C
• rs7104645
• ENST00000796724.1:n.321+470A>C

Variant summary

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

The ENST00000796724.1(ENSG00000303720):​n.321+470A>C 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 0.0 (0 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000303720 ENST00000796724.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.260
• Publications: 1 publications found

Genes affected

ENSG00000303720 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

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
ENSG00000303720	ENST00000796724.1	n.321+470A>C		intron_variant	Intron 2 of 3
ENSG00000303720	ENST00000796725.1	n.298+470A>C		intron_variant	Intron 2 of 3
ENSG00000303720	ENST00000796726.1	n.298+470A>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 1832 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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: AC0 AF: 0.00 AC: 0 AN: 1830 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 896

African (AFR) AF: 0.00 AC: 0 AN: 246

American (AMR) AF: 0.00 AC: 0 AN: 128

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 62

East Asian (EAS) AF: 0.00 AC: 0 AN: 124

South Asian (SAS) AF: 0.00 AC: 0 AN: 54

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 46

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1142

Other (OTH) AF: 0.00 AC: 0 AN: 20

Alfa AF: 0.0239 Hom.: 28

Asia WGS AF: 0.00433 AC: 15 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	2.1
DANN	Benign	0.65
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs7104645; hg19: chr11-2062350;