1-232138386-G-C

Variant names:

• chr1-232138386-G-C
• rs10864721
• ENST00000733245.1:n.202-13690G>C

Variant summary

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

The ENST00000733245.1(ENSG00000235152):​n.202-13690G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 152,040 control chromosomes in the GnomAD database, including 7,598 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 0.29 (7598 hom., cov: 32)
• Consequence: ENSG00000235152 ENST00000733245.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 1 publications found

Genes affected

ENSG00000235152 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.474 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
ENSG00000235152	ENST00000733245.1	n.202-13690G>C		intron_variant	Intron 2 of 7
ENSG00000235152	ENST00000733246.1	n.259-13690G>C		intron_variant	Intron 1 of 2
ENSG00000235152	ENST00000733247.1	n.254-13690G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44270 AN: 151920 Hom.: 7585 Cov.: 32

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.292 AC: 44332 AN: 152040 Hom.: 7598 Cov.: 32 AF XY: 0.288 AC XY: 21400 AN XY: 74306

African (AFR) AF: 0.479 AC: 19864 AN: 41454

American (AMR) AF: 0.218 AC: 3330 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 594 AN: 3464

East Asian (EAS) AF: 0.319 AC: 1650 AN: 5168

South Asian (SAS) AF: 0.208 AC: 1000 AN: 4802

European-Finnish (FIN) AF: 0.209 AC: 2209 AN: 10556

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14806 AN: 67988

Other (OTH) AF: 0.252 AC: 532 AN: 2110

Alfa AF: 0.266 Hom.: 768

Bravo AF: 0.300

Asia WGS AF: 0.251 AC: 878 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	1.9
DANN	Benign	0.35
PhyloP100		0.078

Splicing

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

Other links and lift over

dbSNP: rs10864721; hg19: chr1-232274132; COSMIC: COSV60038385;