5-145148892-T-C

Variant names:

• chr5-145148892-T-C
• rs1981626
• ENST00000659832.1:n.128+79820A>G

Variant summary

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

The ENST00000659832.1(ENSG00000251031):​n.128+79820A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.941 in 152,250 control chromosomes in the GnomAD database, including 67,443 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 0.94 (67443 hom., cov: 33)
• Consequence: ENSG00000251031 ENST00000659832.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.981

Genes affected

ENSG00000251031 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.978 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
ENSG00000251031	ENST00000659832.1	n.128+79820A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.941 AC: 143092 AN: 152132 Hom.: 67384 Cov.: 33

Gnomad AFR AF: 0.986

Gnomad AMI AF: 0.979

Gnomad AMR AF: 0.940

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.842

Gnomad FIN AF: 0.973

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.919

Gnomad OTH AF: 0.924

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

GnomAD4 genome AF: 0.941 AC: 143211 AN: 152250 Hom.: 67443 Cov.: 33 AF XY: 0.942 AC XY: 70075 AN XY: 74426

Gnomad4 AFR AF: 0.986

Gnomad4 AMR AF: 0.940

Gnomad4 ASJ AF: 0.880

Gnomad4 EAS AF: 0.930

Gnomad4 SAS AF: 0.842

Gnomad4 FIN AF: 0.973

Gnomad4 NFE AF: 0.919

Gnomad4 OTH AF: 0.924

Alfa AF: 0.919 Hom.: 69468

Bravo AF: 0.941

Asia WGS AF: 0.886 AC: 3080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1981626; hg19: chr5-144528455;