rs1405051

Positions:

• chr1-72882801-G-A
• chr1-72882801-G-C
• chr1-72882801-G-T

Variant summary

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

The ENST00000668734.1(ENSG00000225087):​n.210+15966C>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 0.466 in 151,844 control chromosomes in the GnomAD database, including 16,787 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 0.47 (16787 hom., cov: 32)
• Consequence: ENST00000668734.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.701 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
	ENST00000668734.1	n.210+15966C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70696 AN: 151728 Hom.: 16788 Cov.: 32

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.466 AC: 70729 AN: 151844 Hom.: 16787 Cov.: 32 AF XY: 0.469 AC XY: 34797 AN XY: 74198

Gnomad4 AFR AF: 0.451

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.489

Gnomad4 EAS AF: 0.720

Gnomad4 SAS AF: 0.572

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.483

Alfa AF: 0.332 Hom.: 883

Bravo AF: 0.460

Asia WGS AF: 0.621 AC: 2158 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.040
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1405051; hg19: chr1-73348484;