rs10206899

chr2-73673773-T-Cchr2-73673773-T-G

Variant summary

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

The NR_003683.2(ALMS1P1):n.738-40T>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 0.228 in 802,780 control chromosomes in the GnomAD database, including 25,374 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 0.30 (8595 hom., cov: 28)
  • Exomes 𝑓: 0.21 (16779 hom.)
• Consequence: ALMS1P1 NR_003683.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.783

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ALMS1P1	NR_003683.2	n.738-40T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALMS1P1	ENST00000428767.1	n.550-40T>C		intron_variant, non_coding_transcript_variant
ALMS1P1	ENST00000450720.5	n.738-40T>C		intron_variant, non_coding_transcript_variant		1
ALMS1P1	ENST00000652439.1	n.795-40T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.303 AC: 44901 AN: 148414 Hom.: 8566 Cov.: 28

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.00492

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.291

GnomAD3 exomes AF: 0.207 AC: 32123 AN: 154944 Hom.: 4250 AF XY: 0.201 AC XY: 16571 AN XY: 82620

Gnomad AFR exome AF: 0.566

Gnomad AMR exome AF: 0.227

Gnomad ASJ exome AF: 0.172

Gnomad EAS exome AF: 0.00365

Gnomad SAS exome AF: 0.151

Gnomad FIN exome AF: 0.188

Gnomad NFE exome AF: 0.223

Gnomad OTH exome AF: 0.203

GnomAD4 exome AF: 0.210 AC: 137720 AN: 654274 Hom.: 16779 Cov.: 9 AF XY: 0.207 AC XY: 71560 AN XY: 345336

Gnomad4 AFR exome AF: 0.545

Gnomad4 AMR exome AF: 0.231

Gnomad4 ASJ exome AF: 0.172

Gnomad4 EAS exome AF: 0.00404

Gnomad4 SAS exome AF: 0.156

Gnomad4 FIN exome AF: 0.183

Gnomad4 NFE exome AF: 0.221

Gnomad4 OTH exome AF: 0.216

GnomAD4 genome AF: 0.303 AC: 44979 AN: 148506 Hom.: 8595 Cov.: 28 AF XY: 0.296 AC XY: 21365 AN XY: 72178

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.00493

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.288

Alfa AF: 0.240 Hom.: 1544

Bravo AF: 0.318

Asia WGS AF: 0.104 AC: 362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.95
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10206899; hg19: chr2-73900900;