rs1785778

Variant names:

• chr18-28683428-G-A
• rs1785778
• ENST00000649159.1:n.66-37509G>A

Variant summary

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

The ENST00000649159.1(ENSG00000265994):​n.66-37509G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.968 in 152,228 control chromosomes in the GnomAD database, including 71,541 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 0.97 (71541 hom., cov: 32)
• Consequence: ENSG00000265994 ENST00000649159.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.428

Genes affected

ENSG00000265994 (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 (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000265994	ENST00000649159.1	n.66-37509G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.969 AC: 147324 AN: 152112 Hom.: 71525 Cov.: 32

Gnomad AFR AF: 0.893

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.987

Gnomad ASJ AF: 0.987

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.995

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.994

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.976

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

GnomAD4 genome AF: 0.968 AC: 147387 AN: 152228 Hom.: 71541 Cov.: 32 AF XY: 0.969 AC XY: 72139 AN XY: 74436

Gnomad4 AFR AF: 0.892

Gnomad4 AMR AF: 0.987

Gnomad4 ASJ AF: 0.987

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.995

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 1.00

Gnomad4 OTH AF: 0.975

Alfa AF: 0.980 Hom.: 9086

Bravo AF: 0.964

Asia WGS AF: 0.984 AC: 3389 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1785778; hg19: chr18-26263392;