rs1304771

Positions:

• chr2-122587484-G-A
• chr2-122587484-G-T

Variant summary

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

The ENST00000657880.1(ENSG00000286481):​n.773+54565G>A 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 0.703 in 151,964 control chromosomes in the GnomAD database, including 37,873 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 0.70 (37873 hom., cov: 31)
• Consequence: ENST00000657880.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.923

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.791 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
	ENST00000657880.1	n.773+54565G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106732 AN: 151846 Hom.: 37832 Cov.: 31

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.703 AC: 106823 AN: 151964 Hom.: 37873 Cov.: 31 AF XY: 0.703 AC XY: 52206 AN XY: 74288

Gnomad4 AFR AF: 0.798

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.652

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.733

Gnomad4 NFE AF: 0.670

Gnomad4 OTH AF: 0.696

Alfa AF: 0.685 Hom.: 6056

Bravo AF: 0.708

Asia WGS AF: 0.610 AC: 2124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.96
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1304771; hg19: chr2-123345060;