18-10121952-G-A

Variant names:

• chr18-10121952-G-A
• rs627953
• ENST00000685786.1:n.389-22205G>A

Variant summary

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

The ENST00000685786.1(ENSG00000265554):​n.389-22205G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 152,136 control chromosomes in the GnomAD database, including 11,323 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 0.36 (11323 hom., cov: 33)
• Consequence: ENSG00000265554 ENST00000685786.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180
• Publications: 3 publications found

Genes affected

ENSG00000265554 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 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
ENSG00000265554	ENST00000685786.1	n.389-22205G>A		intron_variant	Intron 1 of 1
ENSG00000265554	ENST00000751533.1	n.94-22205G>A		intron_variant	Intron 1 of 1
ENSG00000265554	ENST00000751534.1	n.83-3456G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55112 AN: 152018 Hom.: 11299 Cov.: 33

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.363 AC: 55188 AN: 152136 Hom.: 11323 Cov.: 33 AF XY: 0.368 AC XY: 27385 AN XY: 74390

African (AFR) AF: 0.513 AC: 21277 AN: 41502

American (AMR) AF: 0.384 AC: 5866 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1046 AN: 3468

East Asian (EAS) AF: 0.672 AC: 3479 AN: 5176

South Asian (SAS) AF: 0.394 AC: 1898 AN: 4814

European-Finnish (FIN) AF: 0.311 AC: 3291 AN: 10594

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17222 AN: 67980

Other (OTH) AF: 0.354 AC: 748 AN: 2112

Alfa AF: 0.294 Hom.: 22423

Bravo AF: 0.377

Asia WGS AF: 0.548 AC: 1904 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.5
DANN	Benign	0.59
PhyloP100		-0.018

Splicing

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

Other links and lift over

dbSNP: rs627953; hg19: chr18-10121949;