rs4852952

chr2-73642780-T-C

Variant summary

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

The ENST00000652439.1(ALMS1P1):n.243+1455T>C variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.828

Genes affected

ALMS1P1 (HGNC:29586): (ALMS1 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALMS1P1	ENST00000652439.1	n.243+1455T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.551

Gnomad4 ASJ AF: 0.651

Gnomad4 EAS AF: 0.668

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.: 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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4852952; hg19: chr2-73869907;