rs1940989

chr18-27501924-G-A

Variant summary

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

The ENST00000584546.5(ENSG00000264151):n.261-59C>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 0.0711 in 152,328 control chromosomes in the GnomAD database, including 482 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 0.071 (482 hom., cov: 32)
  • Exomes 𝑓: 0.050 (0 hom.)
• Consequence: ENST00000584546.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985126	XR_001753535.1	n.241-59C>T		intron_variant, non_coding_transcript_variant
LOC107985126	XR_001753533.1	n.293-59C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000584546.5	n.261-59C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0711 AC: 10819 AN: 152170 Hom.: 486 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0834

Gnomad ASJ AF: 0.0841

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0366

Gnomad FIN AF: 0.0539

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0526

Gnomad OTH AF: 0.0871

GnomAD4 exome AF: 0.0500 AC: 2 AN: 40 Hom.: 0 AF XY: 0.0385 AC XY: 1 AN XY: 26

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0909

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0711 AC: 10833 AN: 152288 Hom.: 482 Cov.: 32 AF XY: 0.0697 AC XY: 5189 AN XY: 74474

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.0835

Gnomad4 ASJ AF: 0.0841

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0367

Gnomad4 FIN AF: 0.0539

Gnomad4 NFE AF: 0.0527

Gnomad4 OTH AF: 0.0862

Alfa AF: 0.0589 Hom.: 287

Bravo AF: 0.0785

Asia WGS AF: 0.0240 AC: 84 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.1
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1940989; hg19: chr18-25081888;