5-148824199-T-C

Variant names:

• chr5-148824199-T-C
• rs1432622
• ENST00000798472.1:n.254+39T>C

Variant summary

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

The ENST00000798472.1(ENSG00000303969):​n.254+39T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 152,064 control chromosomes in the GnomAD database, including 27,690 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 (27690 hom., cov: 33)
• Consequence: ENSG00000303969 ENST00000798472.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511
• Publications: 18 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000798472.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303969	ENST00000798472.1		n.254+39T>C		intron	N/A
	ENSG00000303969	ENST00000798473.1		n.251+39T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90958 AN: 151946 Hom.: 27671 Cov.: 33

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.599 AC: 91022 AN: 152064 Hom.: 27690 Cov.: 33 AF XY: 0.606 AC XY: 45036 AN XY: 74326

African (AFR) AF: 0.563 AC: 23369 AN: 41478

American (AMR) AF: 0.711 AC: 10869 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.613 AC: 2127 AN: 3472

East Asian (EAS) AF: 0.745 AC: 3854 AN: 5170

South Asian (SAS) AF: 0.741 AC: 3570 AN: 4818

European-Finnish (FIN) AF: 0.632 AC: 6683 AN: 10572

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

European-Non Finnish (NFE) AF: 0.567 AC: 38500 AN: 67946

Other (OTH) AF: 0.630 AC: 1329 AN: 2110

Alfa AF: 0.575 Hom.: 3527

Bravo AF: 0.600

Asia WGS AF: 0.748 AC: 2588 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	13
DANN	Benign	0.74
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs1432622; hg19: chr5-148203762;