rs1001579

Positions:

• chr5-108396257-G-A
• chr5-108396257-G-C
• chr5-108396257-G-T

Variant summary

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

The ENST00000662770.1(ENSG00000286503):​n.253+13849G>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 0.892 in 152,178 control chromosomes in the GnomAD database, including 60,650 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 0.89 (60650 hom., cov: 32)
• Consequence: ENST00000662770.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.838

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.948 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
	ENST00000662770.1	n.253+13849G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.892 AC: 135605 AN: 152060 Hom.: 60596 Cov.: 32

Gnomad AFR AF: 0.956

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.917

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.890

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.893

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

GnomAD4 genome AF: 0.892 AC: 135719 AN: 152178 Hom.: 60650 Cov.: 32 AF XY: 0.892 AC XY: 66355 AN XY: 74372

Gnomad4 AFR AF: 0.956

Gnomad4 AMR AF: 0.918

Gnomad4 ASJ AF: 0.860

Gnomad4 EAS AF: 0.857

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.890

Gnomad4 NFE AF: 0.856

Gnomad4 OTH AF: 0.896

Alfa AF: 0.877 Hom.: 6818

Bravo AF: 0.897

Asia WGS AF: 0.838 AC: 2906 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1001579; hg19: chr5-107731958;