rs3914785

Positions:

• chr18-2452178-A-G
• chr18-2452178-A-T

Variant summary

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

The ENST00000639316.2(ENSG00000263745):​n.268+36981T>C 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 0.854 in 152,074 control chromosomes in the GnomAD database, including 58,207 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 0.85 (58207 hom., cov: 32)
• Consequence: ENST00000639316.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.351

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.983 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000639316.2	n.268+36981T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.854 AC: 129791 AN: 151956 Hom.: 58188 Cov.: 32

Gnomad AFR AF: 0.559

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.998

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.965

Gnomad FIN AF: 0.992

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.990

Gnomad OTH AF: 0.888

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

GnomAD4 genome AF: 0.854 AC: 129864 AN: 152074 Hom.: 58207 Cov.: 32 AF XY: 0.857 AC XY: 63761 AN XY: 74360

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.876

Gnomad4 ASJ AF: 0.998

Gnomad4 EAS AF: 0.835

Gnomad4 SAS AF: 0.965

Gnomad4 FIN AF: 0.992

Gnomad4 NFE AF: 0.990

Gnomad4 OTH AF: 0.887

Alfa AF: 0.935 Hom.: 12961

Bravo AF: 0.830

Asia WGS AF: 0.886 AC: 3063 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.7
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3914785; hg19: chr18-2452177;