chr18-60295884-T-C

Position:

• chr18-60295884-T-C

Variant summary

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

The ENST00000659042.1(ENSG00000267401):​n.515+1211T>C 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 0.236 in 152,162 control chromosomes in the GnomAD database, including 4,881 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 0.24 (4881 hom., cov: 32)
• Consequence: ENST00000659042.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372155	XR_935553.2	n.515+1211T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000659042.1	n.515+1211T>C		intron_variant, non_coding_transcript_variant
	ENST00000592121.2	n.176+1573T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35876 AN: 152044 Hom.: 4882 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.0966

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.236 AC: 35878 AN: 152162 Hom.: 4881 Cov.: 32 AF XY: 0.232 AC XY: 17229 AN XY: 74398

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.0970

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.238

Alfa AF: 0.292 Hom.: 14471

Bravo AF: 0.229

Asia WGS AF: 0.186 AC: 648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.4
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17773430; hg19: chr18-57963117;