chr18-78927314-G-A

Variant names:

• chr18-78927314-G-A
• rs936503
• ENST00000580639.1:n.128C>T

Variant summary

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

The ENST00000580639.1(ENSG00000265101):​n.128C>T 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 0.529 in 152,228 control chromosomes in the GnomAD database, including 22,034 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 0.53 (22026 hom., cov: 35)
  • Exomes 𝑓: 0.79 (8 hom.)
• Consequence: ENSG00000265101 ENST00000580639.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128
• Publications: 4 publications found

Genes affected

ENSG00000265101 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000580639.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000265101	ENST00000580639.1	TSL:3	n.128C>T		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000287758	ENST00000654461.1		n.437+11G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80485 AN: 152082 Hom.: 22024 Cov.: 35

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.550

GnomAD4 exome AF: 0.786 AC: 22 AN: 28 Hom.: 8 Cov.: 0 AF XY: 0.875 AC XY: 14 AN XY: 16

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 2 AN: 4

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.800 AC: 16 AN: 20

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.529 AC: 80515 AN: 152200 Hom.: 22026 Cov.: 35 AF XY: 0.525 AC XY: 39100 AN XY: 74416

African (AFR) AF: 0.394 AC: 16362 AN: 41524

American (AMR) AF: 0.494 AC: 7549 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2090 AN: 3470

East Asian (EAS) AF: 0.451 AC: 2332 AN: 5170

South Asian (SAS) AF: 0.436 AC: 2107 AN: 4830

European-Finnish (FIN) AF: 0.605 AC: 6406 AN: 10596

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41840 AN: 67996

Other (OTH) AF: 0.553 AC: 1168 AN: 2114

Alfa AF: 0.589 Hom.: 114069

Bravo AF: 0.519

Asia WGS AF: 0.442 AC: 1534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.45
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs936503; hg19: chr18-76687314;