2-73642883-C-T

Variant names:

• chr2-73642883-C-T
• rs4852954
• ENST00000652439.1:n.243+1558C>T

Variant summary

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

The ENST00000652439.1(ALMS1P1):​n.243+1558C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 151,844 control chromosomes in the GnomAD database, including 23,073 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 0.52 (23073 hom., cov: 31)
• Consequence: ALMS1P1 ENST00000652439.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581

Genes affected

ALMS1P1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.656 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
ALMS1P1	ENST00000652439.1	n.243+1558C>T		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79283 AN: 151728 Hom.: 23074 Cov.: 31

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.522 AC: 79295 AN: 151844 Hom.: 23073 Cov.: 31 AF XY: 0.530 AC XY: 39297 AN XY: 74214

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.634

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.672

Gnomad4 SAS AF: 0.675

Gnomad4 FIN AF: 0.640

Gnomad4 NFE AF: 0.618

Gnomad4 OTH AF: 0.554

Alfa AF: 0.527 Hom.: 4979

Bravo AF: 0.510

Asia WGS AF: 0.665 AC: 2312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.68
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4852954; hg19: chr2-73870010;