rs7754480

Variant names:

• chr6-114807029-G-A
• rs7754480
• ENST00000751286.1:n.395-15954G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-114807029-G-A
• chr6-114807029-G-C
• chr6-114807029-G-T

Variant summary

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

The ENST00000751286.1(ENSG00000287097):​n.395-15954G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.605 in 151,928 control chromosomes in the GnomAD database, including 29,392 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 0.60 (29392 hom., cov: 31)
• Consequence: ENSG00000287097 ENST00000751286.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.637
• Publications: 2 publications found

Genes affected

ENSG00000287097 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

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
ENSG00000287097	ENST00000751286.1	n.395-15954G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91857 AN: 151810 Hom.: 29387 Cov.: 31

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.605 AC: 91888 AN: 151928 Hom.: 29392 Cov.: 31 AF XY: 0.606 AC XY: 44995 AN XY: 74274

African (AFR) AF: 0.378 AC: 15639 AN: 41382

American (AMR) AF: 0.685 AC: 10462 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2512 AN: 3470

East Asian (EAS) AF: 0.675 AC: 3486 AN: 5162

South Asian (SAS) AF: 0.598 AC: 2881 AN: 4818

European-Finnish (FIN) AF: 0.667 AC: 7036 AN: 10548

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.701 AC: 47678 AN: 67968

Other (OTH) AF: 0.647 AC: 1364 AN: 2108

Alfa AF: 0.640 Hom.: 4173

Bravo AF: 0.597

Asia WGS AF: 0.632 AC: 2198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.44
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs7754480; hg19: chr6-115128193;