rs7000782

Variant names:

• chr8-80395915-T-A
• rs7000782
• ENST00000644465.1:n.254-52782T>A

Variant summary

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

The ENST00000644465.1(ENSG00000253238):​n.254-52782T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 150,036 control chromosomes in the GnomAD database, including 23,418 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 0.54 (23418 hom., cov: 26)
• Consequence: ENSG00000253238 ENST00000644465.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.677
• Publications: 9 publications found

Genes affected

ENSG00000253238 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.735 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
ENSG00000253238	ENST00000644465.1	n.254-52782T>A		intron_variant	Intron 2 of 4
ENSG00000253238	ENST00000656157.2	n.286-86693T>A		intron_variant	Intron 2 of 3
ENSG00000253238	ENST00000656811.1	n.252-6821T>A		intron_variant	Intron 2 of 2
ENSG00000253238	ENST00000662273.2	n.371-86693T>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.540 AC: 80974 AN: 149924 Hom.: 23371 Cov.: 26

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.540 AC: 81081 AN: 150036 Hom.: 23418 Cov.: 26 AF XY: 0.541 AC XY: 39478 AN XY: 73028

African (AFR) AF: 0.742 AC: 30184 AN: 40654

American (AMR) AF: 0.533 AC: 7969 AN: 14962

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1567 AN: 3458

East Asian (EAS) AF: 0.644 AC: 3282 AN: 5100

South Asian (SAS) AF: 0.550 AC: 2623 AN: 4766

European-Finnish (FIN) AF: 0.401 AC: 4024 AN: 10026

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.442 AC: 29948 AN: 67770

Other (OTH) AF: 0.491 AC: 1031 AN: 2098

Alfa AF: 0.493 Hom.: 2419

Bravo AF: 0.561

Asia WGS AF: 0.574 AC: 1997 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.36
DANN	Benign	0.26
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs7000782; hg19: chr8-81308150;