rs758216

chr1-230563488-T-Achr1-230563488-T-C

Variant summary

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

The ENST00000689608.1(ENSG00000282564):n.330-55475T>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 0.13 in 152,230 control chromosomes in the GnomAD database, including 1,565 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 0.13 (1565 hom., cov: 32)
• Consequence: ENST00000689608.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985357	XR_007066934.1	n.171-7127A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000689608.1	n.330-55475T>A		intron_variant, non_coding_transcript_variant
	ENST00000685406.1	n.242-13006T>A		intron_variant, non_coding_transcript_variant
	ENST00000692577.2	n.319-55475T>A		intron_variant, non_coding_transcript_variant
	ENST00000702785.1	n.264-16266T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19768 AN: 152114 Hom.: 1566 Cov.: 32

Gnomad AFR AF: 0.0972

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.0623

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.130 AC: 19766 AN: 152230 Hom.: 1565 Cov.: 32 AF XY: 0.129 AC XY: 9635 AN XY: 74422

Gnomad4 AFR AF: 0.0970

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.0623

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.144

Alfa AF: 0.126 Hom.: 144

Bravo AF: 0.132

Asia WGS AF: 0.317 AC: 1099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	3.5
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs758216; hg19: chr1-230699234;