1-171119518-C-T

Variant summary

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

The ENST00000669750.1(ENSG00000231424):n.533+48586G>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 0.159 in 151,816 control chromosomes in the GnomAD database, including 3,227 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 0.16 (3227 hom., cov: 32)
• Consequence: ENST00000669750.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650

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 = 0.342 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
	ENST00000669750.1	n.533+48586G>A		intron_variant, non_coding_transcript_variant
	ENST00000653116.1	n.542+48586G>A		intron_variant, non_coding_transcript_variant
	ENST00000664920.1	n.681+2232G>A		intron_variant, non_coding_transcript_variant
	ENST00000670085.1	n.371+48586G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24096 AN: 151698 Hom.: 3209 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.0693

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.0410

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0513

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.159 AC: 24162 AN: 151816 Hom.: 3227 Cov.: 32 AF XY: 0.160 AC XY: 11901 AN XY: 74214

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.0693

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.0410

Gnomad4 NFE AF: 0.0513

Gnomad4 OTH AF: 0.143

Alfa AF: 0.0727 Hom.: 652

Bravo AF: 0.181

Asia WGS AF: 0.220 AC: 763 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.79
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9970392; hg19: chr1-171088658;