rs952044

chr18-60130878-C-T

Variant summary

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

The ENST00000588794.1(ENSG00000267686):n.346+1223C>T 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 0.345 in 151,810 control chromosomes in the GnomAD database, including 9,491 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 0.34 (9491 hom., cov: 31)
• Consequence: ENST00000588794.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515

Genes affected

(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 (AFR) allele frequency at 95% confidence interval = 0.434 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
	ENST00000588794.1	n.346+1223C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000668793.1	n.240+1223C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52260 AN: 151692 Hom.: 9483 Cov.: 31

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.345 AC: 52299 AN: 151810 Hom.: 9491 Cov.: 31 AF XY: 0.340 AC XY: 25232 AN XY: 74190

Gnomad4 AFR AF: 0.440

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.338

Alfa AF: 0.318 Hom.: 1796

Bravo AF: 0.347

Asia WGS AF: 0.244 AC: 848 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.4
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs952044; hg19: chr18-57798110;