rs6801020

chr3-152675973-G-A

Variant summary

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

The ENST00000659139.2(ENSG00000287706):n.304-2188G>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 0.111 in 152,028 control chromosomes in the GnomAD database, including 1,870 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 0.11 (1870 hom., cov: 32)
• Consequence: ENST00000659139.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.408

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102724289	XR_924590.3	n.296-2188G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000659139.2	n.304-2188G>A		intron_variant, non_coding_transcript_variant
	ENST00000693350.1	n.251-1141G>A		intron_variant, non_coding_transcript_variant
	ENST00000700832.1	n.280-2188G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16802 AN: 151910 Hom.: 1861 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0581

Gnomad ASJ AF: 0.0196

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.0774

Gnomad FIN AF: 0.0274

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0312

Gnomad OTH AF: 0.0905

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

GnomAD4 genome AF: 0.111 AC: 16837 AN: 152028 Hom.: 1870 Cov.: 32 AF XY: 0.109 AC XY: 8138 AN XY: 74336

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.0579

Gnomad4 ASJ AF: 0.0196

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.0776

Gnomad4 FIN AF: 0.0274

Gnomad4 NFE AF: 0.0312

Gnomad4 OTH AF: 0.0891

Alfa AF: 0.0684 Hom.: 222

Bravo AF: 0.120

Asia WGS AF: 0.139 AC: 485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.92
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: rs6801020; hg19: chr3-152393762;