ENST00000795547.1:n.59+81078C>T

Variant names:

• chr4-187424214-G-A
• rs1431005
• ENST00000795547.1:n.59+81078C>T

Variant summary

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

The ENST00000795547.1(ENSG00000250658):​n.59+81078C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 151,866 control chromosomes in the GnomAD database, including 11,671 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 0.39 (11671 hom., cov: 32)
• Consequence: ENSG00000250658 ENST00000795547.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431
• Publications: 7 publications found

Genes affected

ENSG00000250658 (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 (NFE) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC339975	NR_038931.1	n.322+81078C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000250658	ENST00000795547.1	n.59+81078C>T		intron_variant	Intron 1 of 6
ENSG00000250658	ENST00000795548.1	n.323+81078C>T		intron_variant	Intron 1 of 5
ENSG00000250658	ENST00000795549.1	n.321+81078C>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59097 AN: 151748 Hom.: 11662 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.389 AC: 59125 AN: 151866 Hom.: 11671 Cov.: 32 AF XY: 0.390 AC XY: 28921 AN XY: 74208

African (AFR) AF: 0.365 AC: 15126 AN: 41400

American (AMR) AF: 0.337 AC: 5144 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1327 AN: 3468

East Asian (EAS) AF: 0.378 AC: 1946 AN: 5150

South Asian (SAS) AF: 0.383 AC: 1840 AN: 4808

European-Finnish (FIN) AF: 0.474 AC: 4986 AN: 10518

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27533 AN: 67958

Other (OTH) AF: 0.392 AC: 825 AN: 2102

Alfa AF: 0.396 Hom.: 49202

Bravo AF: 0.377

Asia WGS AF: 0.370 AC: 1286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.48
DANN	Benign	0.62
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs1431005; hg19: chr4-188345368;