5-140594888-T-G

Variant names:

• chr5-140594888-T-G
• rs1864255
• XM_024446282.2:c.-36+27A>C

Variant summary

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

The ENST00000766762.1(ENSG00000293441):​n.155+27A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 151,606 control chromosomes in the GnomAD database, including 20,255 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 (20255 hom., cov: 29)
• Consequence: ENSG00000293441 ENST00000766762.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.496
• Publications: 20 publications found

Genes affected

LOC112267855 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766762.1. 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
	ENSG00000293441	ENST00000766762.1		n.155+27A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77365 AN: 151488 Hom.: 20231 Cov.: 29

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.511 AC: 77435 AN: 151606 Hom.: 20255 Cov.: 29 AF XY: 0.516 AC XY: 38188 AN XY: 74072

African (AFR) AF: 0.442 AC: 18274 AN: 41338

American (AMR) AF: 0.514 AC: 7832 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1905 AN: 3466

East Asian (EAS) AF: 0.455 AC: 2327 AN: 5116

South Asian (SAS) AF: 0.492 AC: 2353 AN: 4784

European-Finnish (FIN) AF: 0.647 AC: 6798 AN: 10510

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.538 AC: 36520 AN: 67852

Other (OTH) AF: 0.500 AC: 1050 AN: 2102

Alfa AF: 0.518 Hom.: 62867

Bravo AF: 0.493

Asia WGS AF: 0.514 AC: 1785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.13
DANN	Benign	0.30
PhyloP100		-0.50

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: rs1864255;

hg19: chr5-139974473;