5-4645342-C-T

Variant names:

• chr5-4645342-C-T
• rs2077369
• ENST00000507435.1:n.430-122975G>A

Variant summary

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

The ENST00000513925.1(ENSG00000251371):​n.356-2728C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 151,888 control chromosomes in the GnomAD database, including 1,558 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 0.12 (1558 hom., cov: 32)
• Consequence: ENSG00000251371 ENST00000513925.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.13
• Publications: 3 publications found

Genes affected

ENSG00000248973 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000513925.1. 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
	ENSG00000248973	ENST00000507435.1	TSL:5	n.430-122975G>A		intron	N/A
	ENSG00000251371	ENST00000513925.1	TSL:3	n.356-2728C>T		intron	N/A
	ENSG00000248973	ENST00000847489.1		n.349-7613G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18149 AN: 151770 Hom.: 1553 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.0275

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.0742

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0563

Gnomad MID AF: 0.0609

Gnomad NFE AF: 0.0732

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.120 AC: 18174 AN: 151888 Hom.: 1558 Cov.: 32 AF XY: 0.123 AC XY: 9151 AN XY: 74242

African (AFR) AF: 0.159 AC: 6564 AN: 41374

American (AMR) AF: 0.273 AC: 4164 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0742 AC: 257 AN: 3464

East Asian (EAS) AF: 0.160 AC: 823 AN: 5158

South Asian (SAS) AF: 0.110 AC: 530 AN: 4804

European-Finnish (FIN) AF: 0.0563 AC: 596 AN: 10580

Middle Eastern (MID) AF: 0.0690 AC: 20 AN: 290

European-Non Finnish (NFE) AF: 0.0732 AC: 4974 AN: 67950

Other (OTH) AF: 0.105 AC: 221 AN: 2104

Alfa AF: 0.0921 Hom.: 1570

Bravo AF: 0.137

Asia WGS AF: 0.152 AC: 528 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.017
DANN	Benign	0.55
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs2077369; hg19: chr5-4645455;