5-40414965-C-T

Variant names:

• chr5-40414965-C-T
• rs1992660
• ENST00000637776.2:n.126C>T

Variant summary

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

The ENST00000637776.2(ENSG00000283286):​n.126C>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 0.571 in 151,854 control chromosomes in the GnomAD database, including 25,439 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 0.57 (25439 hom., cov: 31)
• Consequence: ENSG00000283286 ENST00000637776.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 28 publications found

Genes affected

ENSG00000283286 (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 (AFR) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283286	ENST00000637776.2	n.126C>T		non_coding_transcript_exon_variant	Exon 1 of 2	5
ENSG00000283286	ENST00000809813.1	n.238C>T		non_coding_transcript_exon_variant	Exon 2 of 4
ENSG00000283286	ENST00000809814.1	n.213C>T		non_coding_transcript_exon_variant	Exon 2 of 3

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86615 AN: 151734 Hom.: 25423 Cov.: 31

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.571 AC: 86675 AN: 151854 Hom.: 25439 Cov.: 31 AF XY: 0.563 AC XY: 41786 AN XY: 74166

African (AFR) AF: 0.612 AC: 25349 AN: 41406

American (AMR) AF: 0.475 AC: 7244 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2121 AN: 3466

East Asian (EAS) AF: 0.143 AC: 740 AN: 5166

South Asian (SAS) AF: 0.470 AC: 2259 AN: 4808

European-Finnish (FIN) AF: 0.545 AC: 5718 AN: 10498

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.606 AC: 41164 AN: 67952

Other (OTH) AF: 0.582 AC: 1226 AN: 2108

Alfa AF: 0.585 Hom.: 54924

Bravo AF: 0.564

Asia WGS AF: 0.374 AC: 1302 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.1
DANN	Benign	0.42
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs1992660; hg19: chr5-40415067;