rs1692507

Variant names:

• chr18-28677979-G-A
• rs1692507
• ENST00000649159.1:n.65+39201G>A

Your query was ambiguous. Multiple possible variants found:

• chr18-28677979-G-A
• chr18-28677979-G-C
• chr18-28677979-G-T

Variant summary

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

The ENST00000649159.1(ENSG00000265994):​n.65+39201G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 151,876 control chromosomes in the GnomAD database, including 31,340 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 0.63 (31340 hom., cov: 31)
• Consequence: ENSG00000265994 ENST00000649159.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37
• Publications: 1 publications found

Genes affected

ENSG00000265994 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.769 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+39201G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96252 AN: 151758 Hom.: 31320 Cov.: 31

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.789

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.634 AC: 96318 AN: 151876 Hom.: 31340 Cov.: 31 AF XY: 0.638 AC XY: 47350 AN XY: 74188

African (AFR) AF: 0.492 AC: 20348 AN: 41388

American (AMR) AF: 0.706 AC: 10766 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.752 AC: 2611 AN: 3472

East Asian (EAS) AF: 0.789 AC: 4062 AN: 5146

South Asian (SAS) AF: 0.705 AC: 3395 AN: 4818

European-Finnish (FIN) AF: 0.629 AC: 6613 AN: 10520

Middle Eastern (MID) AF: 0.685 AC: 200 AN: 292

European-Non Finnish (NFE) AF: 0.683 AC: 46390 AN: 67962

Other (OTH) AF: 0.688 AC: 1451 AN: 2110

Alfa AF: 0.651 Hom.: 5495

Bravo AF: 0.634

Asia WGS AF: 0.742 AC: 2580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.16
DANN	Benign	0.53
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs1692507; hg19: chr18-26257943;