rs7670748

Variant names:

• chr4-156142163-G-A
• rs7670748
• ENST00000815672.1:n.366+1589C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-156142163-G-A
• chr4-156142163-G-C
• chr4-156142163-G-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000815672.1(ENSG00000306151):​n.366+1589C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: ENSG00000306151 ENST00000815672.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.837
• Publications: 3 publications found

Genes affected

ENSG00000306151 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724785	XR_001741525.1	n.123+1589C>T		intron_variant	Intron 1 of 5
LOC102724785	XR_427618.3	n.123+1589C>T		intron_variant	Intron 1 of 3
LOC102724785	XR_939391.2	n.123+1589C>T		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306151	ENST00000815672.1	n.366+1589C>T		intron_variant	Intron 1 of 3
ENSG00000306151	ENST00000815673.1	n.252+1589C>T		intron_variant	Intron 1 of 2
ENSG00000306151	ENST00000815674.1	n.191+1589C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 6732

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.81
DANN	Benign	0.91
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs7670748; hg19: chr4-157063315;