rs437749

chr1-82788115-G-A

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, non coding transcript 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: ENST00000650063.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.811

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650063.1	n.265+25999C>T		intron_variant, non_coding_transcript_variant
	ENST00000653483.1	n.97+25999C>T		intron_variant, non_coding_transcript_variant
	ENST00000663002.1	n.93+25999C>T		intron_variant, non_coding_transcript_variant
	ENST00000702694.1	n.93+25999C>T		intron_variant, non_coding_transcript_variant

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;