rs1692506

Variant names:

• chr18-28677902-T-A
• rs1692506
• ENST00000649159.1:n.65+39124T>A

Your query was ambiguous. Multiple possible variants found:

• chr18-28677902-T-A
• chr18-28677902-T-G

Variant summary

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

The ENST00000649159.1(ENSG00000265994):​n.65+39124T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.598 in 151,978 control chromosomes in the GnomAD database, including 28,665 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 0.60 (28665 hom., cov: 31)
• Consequence: ENSG00000265994 ENST00000649159.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137

Genes affected

ENSG00000265994 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.768 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.65+39124T>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90896 AN: 151860 Hom.: 28655 Cov.: 31

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.598 AC: 90942 AN: 151978 Hom.: 28665 Cov.: 31 AF XY: 0.603 AC XY: 44811 AN XY: 74256

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.674

Gnomad4 ASJ AF: 0.743

Gnomad4 EAS AF: 0.788

Gnomad4 SAS AF: 0.698

Gnomad4 FIN AF: 0.627

Gnomad4 NFE AF: 0.674

Gnomad4 OTH AF: 0.654

Alfa AF: 0.623 Hom.: 3776

Bravo AF: 0.593

Asia WGS AF: 0.730 AC: 2537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1692506; hg19: chr18-26257866;