rs1940989

Variant names:

• chr18-27501924-G-A
• rs1940989
• ENST00000584546.5:n.261-59C>T

Variant summary

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

The ENST00000584546.5(ENSG00000264151):​n.261-59C>T variant causes a intron 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: ENSG00000264151 ENST00000584546.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 2 publications found

Genes affected

ENSG00000264151 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC107985126	XR_001753533.1	n.293-59C>T		intron_variant	Intron 3 of 3
LOC107985126	XR_001753535.1	n.241-59C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000264151	ENST00000584546.5	n.261-59C>T		intron_variant	Intron 2 of 4	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

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: 0.00 AC: 0 AN: 12

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0909 AC: 2 AN: 22

Other (OTH) AF: 0.00 AC: 0 AN: 6

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

African (AFR) AF: 0.113 AC: 4696 AN: 41552

American (AMR) AF: 0.0835 AC: 1278 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0841 AC: 292 AN: 3470

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5180

South Asian (SAS) AF: 0.0367 AC: 177 AN: 4828

European-Finnish (FIN) AF: 0.0539 AC: 573 AN: 10624

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0527 AC: 3582 AN: 68018

Other (OTH) AF: 0.0862 AC: 182 AN: 2112

Alfa AF: 0.0627 Hom.: 581

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
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs1940989; hg19: chr18-25081888;