1-171119518-C-T

Variant names:

• chr1-171119518-C-T
• rs9970392
• ENST00000653116.1:n.542+48586G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000653116.1(ENSG00000231424):​n.542+48586G>A variant causes a intron 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: ENSG00000231424 ENST00000653116.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650
• Publications: 2 publications found

Genes affected

ENSG00000231424 (HGNC:40240):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231424	ENST00000653116.1	n.542+48586G>A		intron_variant	Intron 3 of 3
ENSG00000231424	ENST00000664920.1	n.681+2232G>A		intron_variant	Intron 4 of 5
ENSG00000231424	ENST00000669750.1	n.533+48586G>A		intron_variant	Intron 3 of 4
ENSG00000231424	ENST00000670085.1	n.371+48586G>A		intron_variant	Intron 2 of 3

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

African (AFR) AF: 0.346 AC: 14324 AN: 41358

American (AMR) AF: 0.219 AC: 3342 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.0693 AC: 240 AN: 3464

East Asian (EAS) AF: 0.188 AC: 971 AN: 5154

South Asian (SAS) AF: 0.193 AC: 929 AN: 4808

European-Finnish (FIN) AF: 0.0410 AC: 433 AN: 10566

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0513 AC: 3482 AN: 67918

Other (OTH) AF: 0.143 AC: 301 AN: 2106

Alfa AF: 0.0867 Hom.: 1260

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
PhyloP100		-0.065

Splicing

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

Other links and lift over

dbSNP: rs9970392; hg19: chr1-171088658;