5-4035819-T-C

Variant names:

• chr5-4035819-T-C
• rs521660
• ENST00000506305.1:n.279+1416A>G

Variant summary

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

The ENST00000506305.1(ENSG00000249994):​n.279+1416A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 151,986 control chromosomes in the GnomAD database, including 29,624 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 0.61 (29624 hom., cov: 32)
• Consequence: ENSG00000249994 ENST00000506305.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263
• Publications: 2 publications found

Genes affected

ENSG00000249994 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000506305.1. 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
	ENSG00000249994	ENST00000506305.1	TSL:3	n.279+1416A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92894 AN: 151866 Hom.: 29585 Cov.: 32

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.612 AC: 92984 AN: 151986 Hom.: 29624 Cov.: 32 AF XY: 0.615 AC XY: 45653 AN XY: 74282

African (AFR) AF: 0.788 AC: 32675 AN: 41456

American (AMR) AF: 0.586 AC: 8943 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2124 AN: 3468

East Asian (EAS) AF: 0.769 AC: 3968 AN: 5160

South Asian (SAS) AF: 0.610 AC: 2938 AN: 4818

European-Finnish (FIN) AF: 0.566 AC: 5980 AN: 10560

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.507 AC: 34462 AN: 67966

Other (OTH) AF: 0.601 AC: 1264 AN: 2104

Alfa AF: 0.570 Hom.: 3284

Bravo AF: 0.622

Asia WGS AF: 0.679 AC: 2361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.46
PhyloP100		-0.26

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs521660;

hg19: chr5-4035932;