5-132537173-A-C

Variant names:

• chr5-132537173-A-C
• rs739719
• ENST00000638452.2:c.-168-22111A>C

Variant summary

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

The ENST00000638452.2(ENSG00000283782):​c.-168-22111A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.785 in 152,158 control chromosomes in the GnomAD database, including 50,608 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 0.78 (50608 hom., cov: 32)
• Consequence: ENSG00000283782 ENST00000638452.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100
• Publications: 34 publications found

Genes affected

ENSG00000283782 (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 (NFE) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000638452.2. 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
	ENSG00000283782	ENST00000638452.2	TSL:5	c.-168-22111A>C		intron	N/A	ENSP00000492349.2
	ENSG00000283782	ENST00000638568.2	TSL:5	c.-310-19159A>C		intron	N/A	ENSP00000491158.2
	ENSG00000283782	ENST00000640655.2	TSL:5	c.-168-22111A>C		intron	N/A	ENSP00000491596.2

Frequencies

GnomAD3 genomes AF: 0.785 AC: 119362 AN: 152040 Hom.: 50597 Cov.: 32

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.952

Gnomad AMR AF: 0.884

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.770

Gnomad SAS AF: 0.905

Gnomad FIN AF: 0.959

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.933

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.785 AC: 119393 AN: 152158 Hom.: 50608 Cov.: 32 AF XY: 0.789 AC XY: 58677 AN XY: 74390

African (AFR) AF: 0.432 AC: 17918 AN: 41454

American (AMR) AF: 0.884 AC: 13512 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.897 AC: 3114 AN: 3470

East Asian (EAS) AF: 0.771 AC: 3992 AN: 5180

South Asian (SAS) AF: 0.906 AC: 4367 AN: 4820

European-Finnish (FIN) AF: 0.959 AC: 10186 AN: 10622

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.933 AC: 63472 AN: 68018

Other (OTH) AF: 0.823 AC: 1735 AN: 2108

Alfa AF: 0.889 Hom.: 258663

Bravo AF: 0.762

Asia WGS AF: 0.814 AC: 2832 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.61
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs739719; hg19: chr5-131872865;