18-60169647-T-C

Variant names:

• chr18-60169647-T-C
• rs2051311
• ENST00000764630.1:n.976A>G

Variant summary

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

The ENST00000764630.1(ENSG00000299555):​n.976A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 152,072 control chromosomes in the GnomAD database, including 21,801 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 0.51 (21801 hom., cov: 32)
• Consequence: ENSG00000299555 ENST00000764630.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198
• Publications: 6 publications found

Genes affected

ENSG00000299555 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000764630.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299555	ENST00000764630.1		n.976A>G		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000299555	ENST00000764631.1		n.1112A>G		non_coding_transcript_exon	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77450 AN: 151954 Hom.: 21767 Cov.: 32

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.510 AC: 77533 AN: 152072 Hom.: 21801 Cov.: 32 AF XY: 0.504 AC XY: 37481 AN XY: 74364

African (AFR) AF: 0.754 AC: 31247 AN: 41468

American (AMR) AF: 0.379 AC: 5792 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1140 AN: 3470

East Asian (EAS) AF: 0.210 AC: 1087 AN: 5184

South Asian (SAS) AF: 0.520 AC: 2504 AN: 4820

European-Finnish (FIN) AF: 0.428 AC: 4525 AN: 10570

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29725 AN: 67964

Other (OTH) AF: 0.466 AC: 984 AN: 2110

Alfa AF: 0.449 Hom.: 23199

Bravo AF: 0.513

Asia WGS AF: 0.365 AC: 1269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.6
DANN	Benign	0.82
PhyloP100		0.20

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2051311;

hg19: chr18-57836880;