rs1882095

Variant names:

• chr7-129757804-T-C
• rs1882095
• ENST00000720939.1:n.350+4544A>G

Variant summary

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

The ENST00000720939.1(ENSG00000294095):​n.350+4544A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.587 in 151,902 control chromosomes in the GnomAD database, including 26,848 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 (26848 hom., cov: 31)
• Consequence: ENSG00000294095 ENST00000720939.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810
• Publications: 10 publications found

Genes affected

ENSG00000294095 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.655 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
ENSG00000294095	ENST00000720939.1	n.350+4544A>G		intron_variant	Intron 1 of 1
ENSG00000294095	ENST00000720940.1	n.350+4544A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.587 AC: 89150 AN: 151784 Hom.: 26837 Cov.: 31

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.587 AC: 89171 AN: 151902 Hom.: 26848 Cov.: 31 AF XY: 0.585 AC XY: 43448 AN XY: 74236

African (AFR) AF: 0.496 AC: 20546 AN: 41412

American (AMR) AF: 0.580 AC: 8859 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.728 AC: 2522 AN: 3466

East Asian (EAS) AF: 0.278 AC: 1429 AN: 5140

South Asian (SAS) AF: 0.547 AC: 2631 AN: 4812

European-Finnish (FIN) AF: 0.604 AC: 6360 AN: 10522

Middle Eastern (MID) AF: 0.589 AC: 172 AN: 292

European-Non Finnish (NFE) AF: 0.660 AC: 44863 AN: 67952

Other (OTH) AF: 0.566 AC: 1196 AN: 2112

Alfa AF: 0.641 Hom.: 45115

Bravo AF: 0.578

Asia WGS AF: 0.384 AC: 1332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.3
DANN	Benign	0.82
PhyloP100		-0.081

Splicing

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

Other links and lift over

dbSNP: rs1882095; hg19: chr7-129397644;