chr5-32830415-T-C

Variant names:

• chr5-32830415-T-C
• rs1173727
• ENST00000841800.1:n.496-19320A>G

Variant summary

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

The ENST00000841800.1(ENSG00000250697):​n.496-19320A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 152,136 control chromosomes in the GnomAD database, including 33,024 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 0.65 (33024 hom., cov: 33)
• Consequence: ENSG00000250697 ENST00000841800.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 47 publications found

Genes affected

ENSG00000250697 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.788 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
ENSG00000250697	ENST00000841800.1	n.496-19320A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.651 AC: 99029 AN: 152020 Hom.: 32972 Cov.: 33

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.652 AC: 99136 AN: 152136 Hom.: 33024 Cov.: 33 AF XY: 0.649 AC XY: 48278 AN XY: 74360

African (AFR) AF: 0.795 AC: 33005 AN: 41504

American (AMR) AF: 0.602 AC: 9211 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.582 AC: 2020 AN: 3472

East Asian (EAS) AF: 0.648 AC: 3349 AN: 5168

South Asian (SAS) AF: 0.583 AC: 2813 AN: 4826

European-Finnish (FIN) AF: 0.591 AC: 6246 AN: 10570

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.595 AC: 40428 AN: 67992

Other (OTH) AF: 0.641 AC: 1354 AN: 2112

Alfa AF: 0.612 Hom.: 89003

Bravo AF: 0.658

Asia WGS AF: 0.639 AC: 2221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.034
DANN	Benign	0.45
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1173727; hg19: chr5-32830521;