rs437749

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

ENSG00000233290 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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	ENST00000663002.2	n.93+25999C>T		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.445 AC: 18418 AN: 41418

American (AMR) AF: 0.309 AC: 4715 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1856 AN: 3468

East Asian (EAS) AF: 0.133 AC: 686 AN: 5172

South Asian (SAS) AF: 0.378 AC: 1823 AN: 4826

European-Finnish (FIN) AF: 0.357 AC: 3773 AN: 10558

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.402 AC: 27309 AN: 67934

Other (OTH) AF: 0.429 AC: 904 AN: 2106

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
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs437749; hg19: chr1-83253798;