2-73642781-G-A

Variant names:

• chr2-73642781-G-A
• rs4852953
• ENST00000652439.1:n.243+1456G>A

Variant summary

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

The ENST00000652439.1(ALMS1P1):​n.243+1456G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 151,442 control chromosomes in the GnomAD database, including 22,731 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 0.51 (22731 hom., cov: 31)
• Consequence: ALMS1P1 ENST00000652439.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13

Genes affected

ALMS1P1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.662 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+1456G>A		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77377 AN: 151324 Hom.: 22737 Cov.: 31

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.511 AC: 77373 AN: 151442 Hom.: 22731 Cov.: 31 AF XY: 0.517 AC XY: 38235 AN XY: 73940

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.551

Gnomad4 ASJ AF: 0.651

Gnomad4 EAS AF: 0.667

Gnomad4 SAS AF: 0.682

Gnomad4 FIN AF: 0.640

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.548

Alfa AF: 0.568 Hom.: 3287

Bravo AF: 0.489

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.1
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4852953; hg19: chr2-73869908;