5-140594888-T-G

Variant names:

• chr5-140594888-T-G
• rs1864255
• ENST00000766762.1:n.155+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

ENSG00000293441 (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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112267855	XM_024446282.2	c.-36+27A>C		intron_variant	Intron 1 of 8		XP_024302050.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293441	ENST00000766762.1	n.155+27A>C		intron_variant	Intron 1 of 6

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 v4.3

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

Other links and lift over

dbSNP: rs1864255; hg19: chr5-139974473;