5-135910088-A-G

Variant names:

• chr5-135910088-A-G
• rs740002
• ENST00000523722.1:n.240-266T>C

Variant summary

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

The ENST00000523722.1(ENSG00000253927):​n.240-266T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 151,072 control chromosomes in the GnomAD database, including 7,665 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 0.31 (7665 hom., cov: 28)
• Consequence: ENSG00000253927 ENST00000523722.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.130
• Publications: 5 publications found

Genes affected

ENSG00000253927 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000523722.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253927	ENST00000523722.1	TSL:3	n.240-266T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46398 AN: 150954 Hom.: 7661 Cov.: 28

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.307 AC: 46425 AN: 151072 Hom.: 7665 Cov.: 28 AF XY: 0.310 AC XY: 22860 AN XY: 73728

African (AFR) AF: 0.178 AC: 7324 AN: 41136

American (AMR) AF: 0.366 AC: 5543 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1150 AN: 3458

East Asian (EAS) AF: 0.473 AC: 2416 AN: 5108

South Asian (SAS) AF: 0.408 AC: 1929 AN: 4724

European-Finnish (FIN) AF: 0.319 AC: 3322 AN: 10410

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23636 AN: 67768

Other (OTH) AF: 0.337 AC: 710 AN: 2106

Alfa AF: 0.335 Hom.: 19419

Bravo AF: 0.305

Asia WGS AF: 0.428 AC: 1490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.1
DANN	Benign	0.81
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs740002; hg19: chr5-135245777;