rs788748

Variant names:

• chr7-45986582-A-G
• rs788748
• ENST00000797062.1:n.406+6555A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-45986582-A-G
• chr7-45986582-A-T

Variant summary

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

The ENST00000797062.1(ENSG00000237471):​n.406+6555A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 152,058 control chromosomes in the GnomAD database, including 27,561 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 0.59 (27561 hom., cov: 32)
• Consequence: ENSG00000237471 ENST00000797062.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179
• Publications: 12 publications found

Genes affected

ENSG00000237471 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.892 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723446	NR_187744.1	n.671-3951A>G		intron_variant	Intron 3 of 3
LOC102723446	NR_187745.1	n.*110A>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000237471	ENST00000797062.1	n.406+6555A>G		intron_variant	Intron 3 of 3
ENSG00000237471	ENST00000797063.1	n.671-3951A>G		intron_variant	Intron 3 of 3
ENSG00000237471	ENST00000797064.1	n.136-3951A>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89763 AN: 151940 Hom.: 27529 Cov.: 32

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.914

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.591 AC: 89848 AN: 152058 Hom.: 27561 Cov.: 32 AF XY: 0.592 AC XY: 44003 AN XY: 74312

African (AFR) AF: 0.733 AC: 30416 AN: 41490

American (AMR) AF: 0.533 AC: 8149 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2070 AN: 3468

East Asian (EAS) AF: 0.913 AC: 4708 AN: 5154

South Asian (SAS) AF: 0.613 AC: 2954 AN: 4820

European-Finnish (FIN) AF: 0.504 AC: 5326 AN: 10574

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.506 AC: 34404 AN: 67958

Other (OTH) AF: 0.582 AC: 1225 AN: 2104

Alfa AF: 0.545 Hom.: 49331

Bravo AF: 0.596

Asia WGS AF: 0.734 AC: 2550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.76
DANN	Benign	0.58
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs788748; hg19: chr7-46026181;