5-146369972-A-G

Variant names:

• chr5-146369972-A-G
• rs7718446
• ENST00000511390.1:n.83+5371T>C

Variant summary

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

The ENST00000511390.1(ENSG00000250025):​n.83+5371T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 152,046 control chromosomes in the GnomAD database, including 13,512 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 0.39 (13512 hom., cov: 32)
• Consequence: ENSG00000250025 ENST00000511390.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.141
• Publications: 8 publications found

Genes affected

ENSG00000250025 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.627 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
ENSG00000250025	ENST00000511390.1	n.83+5371T>C		intron_variant	Intron 1 of 2	3
ENSG00000250025	ENST00000515598.1	n.403+5371T>C		intron_variant	Intron 2 of 2	3
ENSG00000250025	ENST00000739917.1	n.771+615T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59113 AN: 151928 Hom.: 13473 Cov.: 32

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.389 AC: 59200 AN: 152046 Hom.: 13512 Cov.: 32 AF XY: 0.387 AC XY: 28733 AN XY: 74326

African (AFR) AF: 0.633 AC: 26253 AN: 41442

American (AMR) AF: 0.315 AC: 4808 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1022 AN: 3468

East Asian (EAS) AF: 0.459 AC: 2373 AN: 5172

South Asian (SAS) AF: 0.168 AC: 812 AN: 4820

European-Finnish (FIN) AF: 0.306 AC: 3232 AN: 10572

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.285 AC: 19342 AN: 67976

Other (OTH) AF: 0.370 AC: 781 AN: 2112

Alfa AF: 0.322 Hom.: 29118

Bravo AF: 0.409

Asia WGS AF: 0.329 AC: 1144 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	5.2
DANN	Benign	0.53
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs7718446; hg19: chr5-145749535;