rs1331046

Variant names:

• chr1-232133407-C-A
• rs1331046
• ENST00000733245.1:n.201+12678C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-232133407-C-A
• chr1-232133407-C-T

Variant summary

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

The ENST00000733245.1(ENSG00000235152):​n.201+12678C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0473 in 152,160 control chromosomes in the GnomAD database, including 262 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 0.047 (262 hom., cov: 32)
• Consequence: ENSG00000235152 ENST00000733245.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.186 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.201+12678C>A		intron_variant	Intron 2 of 7
ENSG00000235152	ENST00000733246.1	n.258+12678C>A		intron_variant	Intron 1 of 2
ENSG00000235152	ENST00000733247.1	n.253+14694C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0473 AC: 7193 AN: 152042 Hom.: 261 Cov.: 32

Gnomad AFR AF: 0.0277

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.0613

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.0365

Gnomad FIN AF: 0.0516

Gnomad MID AF: 0.00955

Gnomad NFE AF: 0.0442

Gnomad OTH AF: 0.0480

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

GnomAD4 genome AF: 0.0473 AC: 7204 AN: 152160 Hom.: 262 Cov.: 32 AF XY: 0.0491 AC XY: 3650 AN XY: 74378

African (AFR) AF: 0.0277 AC: 1151 AN: 41512

American (AMR) AF: 0.0615 AC: 940 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0314 AC: 109 AN: 3470

East Asian (EAS) AF: 0.196 AC: 1011 AN: 5162

South Asian (SAS) AF: 0.0367 AC: 177 AN: 4818

European-Finnish (FIN) AF: 0.0516 AC: 546 AN: 10590

Middle Eastern (MID) AF: 0.0103 AC: 3 AN: 292

European-Non Finnish (NFE) AF: 0.0442 AC: 3004 AN: 68004

Other (OTH) AF: 0.0484 AC: 102 AN: 2106

Alfa AF: 0.0443 Hom.: 348

Bravo AF: 0.0487

Asia WGS AF: 0.0930 AC: 324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.75
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs1331046; hg19: chr1-232269153;