rs4852952

Variant names:

• chr2-73642780-T-C
• rs4852952
• ENST00000652439.1:n.243+1455T>C

Variant summary

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

The ENST00000652439.1(ALMS1P1):​n.243+1455T>C 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 151,464 control chromosomes in the GnomAD database, including 22,735 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 (22735 hom., cov: 31)
• Consequence: ALMS1P1 ENST00000652439.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.828
• Publications: 2 publications found

Genes affected

ALMS1P1 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• 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+1455T>C		intron_variant	Intron 1 of 6
ALMS1P1	ENST00000755937.1	n.405+1544T>C		intron_variant	Intron 1 of 1
ALMS1P1	ENST00000755941.1	n.603+1455T>C		intron_variant	Intron 1 of 5
ALMS1P1	ENST00000755942.1	n.553+1455T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77392 AN: 151346 Hom.: 22741 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: 0.646

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: 77388 AN: 151464 Hom.: 22735 Cov.: 31 AF XY: 0.517 AC XY: 38243 AN XY: 73970

African (AFR) AF: 0.197 AC: 8152 AN: 41432

American (AMR) AF: 0.551 AC: 8365 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2243 AN: 3444

East Asian (EAS) AF: 0.668 AC: 3403 AN: 5098

South Asian (SAS) AF: 0.682 AC: 3280 AN: 4810

European-Finnish (FIN) AF: 0.640 AC: 6711 AN: 10482

Middle Eastern (MID) AF: 0.640 AC: 187 AN: 292

European-Non Finnish (NFE) AF: 0.639 AC: 43276 AN: 67734

Other (OTH) AF: 0.548 AC: 1148 AN: 2096

Alfa AF: 0.568 Hom.: 3288

Bravo AF: 0.490

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.097
DANN	Benign	0.16
PhyloP100		-0.83
PromoterAI		0.031	Neutral

Splicing

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

Other links and lift over

dbSNP: rs4852952; hg19: chr2-73869907;