rs1251584

Positions:

• chr1-75958755-T-C

Variant summary

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

The ENST00000663316.1(ENSG00000225605):​n.349-13465T>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 0.226 in 152,100 control chromosomes in the GnomAD database, including 4,552 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 0.23 (4552 hom., cov: 31)
• Consequence: ENST00000663316.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0540

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000663316.1	n.349-13465T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34400 AN: 151982 Hom.: 4549 Cov.: 31

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.0297

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.226 AC: 34403 AN: 152100 Hom.: 4552 Cov.: 31 AF XY: 0.227 AC XY: 16859 AN XY: 74354

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.0299

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.275

Alfa AF: 0.256 Hom.: 937

Bravo AF: 0.219

Asia WGS AF: 0.135 AC: 471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1251584; hg19: chr1-76424440;