chr4-18519037-G-A

Position:

• chr4-18519037-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000652661.1(ENSG00000286046):​n.418+30064G>A variant causes a intron, non coding transcript 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: ENST00000652661.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374510	XR_001741602.2	n.90+107147G>A		intron_variant, non_coding_transcript_variant
LOC105374510	XR_001741601.2	n.822+30092G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000652661.1	n.418+30064G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.775

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.622

Alfa AF: 0.458 Hom.: 1257

Bravo AF: 0.624

Asia WGS AF: 0.605 AC: 2104 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2643435; hg19: chr4-18520660;