chr4-18519037-G-A

Variant names:

• chr4-18519037-G-A
• rs2643435
• ENST00000652661.1:n.418+30064G>A

Variant summary

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

The ENST00000652661.1(ENSG00000286046):​n.418+30064G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 151,816 control chromosomes in the GnomAD database, including 29,014 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 (29014 hom., cov: 31)
• Consequence: ENSG00000286046 ENST00000652661.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636
• Publications: 0 publications found

Genes affected

ENSG00000286046 (HGNC:59078):

LOC105374510 (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 = 0.768 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652661.1. 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
	ENSG00000286046	ENST00000652661.1		n.418+30064G>A		intron	N/A
	ENSG00000286046	ENST00000767385.1		n.175+30092G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.607 AC: 92141 AN: 151700 Hom.: 28975 Cov.: 31

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.608 AC: 92230 AN: 151816 Hom.: 29014 Cov.: 31 AF XY: 0.597 AC XY: 44275 AN XY: 74180

African (AFR) AF: 0.775 AC: 32135 AN: 41474

American (AMR) AF: 0.525 AC: 7985 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2211 AN: 3462

East Asian (EAS) AF: 0.521 AC: 2664 AN: 5110

South Asian (SAS) AF: 0.592 AC: 2849 AN: 4816

European-Finnish (FIN) AF: 0.392 AC: 4139 AN: 10554

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.564 AC: 38255 AN: 67864

Other (OTH) AF: 0.622 AC: 1314 AN: 2112

Alfa AF: 0.481 Hom.: 1492

Bravo AF: 0.624

Asia WGS AF: 0.605 AC: 2104 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.75
PhyloP100		-0.64

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: rs2643435;

hg19: chr4-18520660;