rs437749

Variant names:

• chr1-82788115-G-A
• rs437749
• ENST00000650063.1:n.265+25999C>T

Variant summary

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

The ENST00000650063.1(ENSG00000233290):​n.265+25999C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 151,948 control chromosomes in the GnomAD database, including 12,314 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 0.40 (12314 hom., cov: 32)
• Consequence: ENSG00000233290 ENST00000650063.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.811

Genes affected

ENSG00000233290 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.439 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
ENSG00000233290	ENST00000650063.1	n.265+25999C>T		intron_variant	Intron 3 of 6
ENSG00000233290	ENST00000653483.1	n.97+25999C>T		intron_variant	Intron 1 of 4
ENSG00000233290	ENST00000663002.1	n.93+25999C>T		intron_variant	Intron 1 of 3
ENSG00000233290	ENST00000702694.1	n.93+25999C>T		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59991 AN: 151830 Hom.: 12296 Cov.: 32

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.395 AC: 60049 AN: 151948 Hom.: 12314 Cov.: 32 AF XY: 0.389 AC XY: 28913 AN XY: 74238

Gnomad4 AFR AF: 0.445

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.429

Alfa AF: 0.396 Hom.: 1547

Bravo AF: 0.393

Asia WGS AF: 0.289 AC: 1008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.23
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs437749; hg19: chr1-83253798;