7-46001501-A-G

Variant names:

• chr7-46001501-A-G
• rs788740
• ENST00000797156.1:n.81-5369T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000797156.1(ENSG00000303781):​n.81-5369T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.766 in 152,124 control chromosomes in the GnomAD database, including 45,048 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 0.77 (45048 hom., cov: 33)
• Consequence: ENSG00000303781 ENST00000797156.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 6 publications found

Genes affected

ENSG00000303781 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375264	XR_001745204.2	n.145-5369T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303781	ENST00000797156.1	n.81-5369T>C		intron_variant	Intron 1 of 4
ENSG00000303781	ENST00000797157.1	n.66-667T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.767 AC: 116514 AN: 152006 Hom.: 45020 Cov.: 33

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.883

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.886

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.766 AC: 116598 AN: 152124 Hom.: 45048 Cov.: 33 AF XY: 0.764 AC XY: 56835 AN XY: 74358

African (AFR) AF: 0.743 AC: 30843 AN: 41492

American (AMR) AF: 0.742 AC: 11353 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.883 AC: 3065 AN: 3470

East Asian (EAS) AF: 0.986 AC: 5111 AN: 5182

South Asian (SAS) AF: 0.886 AC: 4280 AN: 4828

European-Finnish (FIN) AF: 0.667 AC: 7046 AN: 10562

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.768 AC: 52232 AN: 67978

Other (OTH) AF: 0.805 AC: 1698 AN: 2110

Alfa AF: 0.775 Hom.: 52879

Bravo AF: 0.768

Asia WGS AF: 0.924 AC: 3207 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.8
DANN	Benign	0.54
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs788740; hg19: chr7-46041100;