chr5-148824445-C-T

Variant names:

• chr5-148824445-C-T
• rs1432623
• ENST00000798472.1:n.254+285C>T

Variant summary

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

The ENST00000798472.1(ENSG00000303969):​n.254+285C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.598 in 152,070 control chromosomes in the GnomAD database, including 27,641 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 (27641 hom., cov: 33)
• Consequence: ENSG00000303969 ENST00000798472.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• Publications: 9 publications found

Genes affected

ENSG00000303969 (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 (EAS) allele frequency at 95% confidence interval = 0.726 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
ENSG00000303969	ENST00000798472.1	n.254+285C>T		intron_variant	Intron 2 of 4
ENSG00000303969	ENST00000798473.1	n.251+285C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90894 AN: 151952 Hom.: 27622 Cov.: 33

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.598 AC: 90958 AN: 152070 Hom.: 27641 Cov.: 33 AF XY: 0.606 AC XY: 45044 AN XY: 74356

African (AFR) AF: 0.563 AC: 23358 AN: 41458

American (AMR) AF: 0.711 AC: 10867 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2124 AN: 3472

East Asian (EAS) AF: 0.745 AC: 3864 AN: 5184

South Asian (SAS) AF: 0.741 AC: 3579 AN: 4828

European-Finnish (FIN) AF: 0.634 AC: 6698 AN: 10568

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.565 AC: 38418 AN: 67956

Other (OTH) AF: 0.629 AC: 1329 AN: 2114

Alfa AF: 0.574 Hom.: 3521

Bravo AF: 0.599

Asia WGS AF: 0.749 AC: 2600 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	0.042
DANN	Benign	0.32
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1432623; hg19: chr5-148204008;