rs1033540

Variant names:

• chr6-131416162-C-T
• rs1033540
• ENST00000702750.2:n.303+23968G>A

Variant summary

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

The ENST00000702750.2(ENSG00000290067):​n.303+23968G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 152,042 control chromosomes in the GnomAD database, including 6,040 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 0.27 (6040 hom., cov: 32)
• Consequence: ENSG00000290067 ENST00000702750.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609
• Publications: 4 publications found

Genes affected

ENSG00000290067 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378005	XR_001744344.2	n.275+23968G>A		intron_variant	Intron 3 of 4
LOC105378005	XR_007059769.1	n.526+23968G>A		intron_variant	Intron 2 of 3
LOC105378005	XR_007059770.1	n.542+23968G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290067	ENST00000702750.2	n.303+23968G>A		intron_variant	Intron 3 of 4
ENSG00000290067	ENST00000771190.1	n.292+23968G>A		intron_variant	Intron 3 of 4
ENSG00000290067	ENST00000771191.1	n.298+23968G>A		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41163 AN: 151924 Hom.: 6033 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.271 AC: 41181 AN: 152042 Hom.: 6040 Cov.: 32 AF XY: 0.272 AC XY: 20200 AN XY: 74304

African (AFR) AF: 0.154 AC: 6380 AN: 41472

American (AMR) AF: 0.295 AC: 4507 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1074 AN: 3470

East Asian (EAS) AF: 0.177 AC: 918 AN: 5172

South Asian (SAS) AF: 0.374 AC: 1802 AN: 4812

European-Finnish (FIN) AF: 0.327 AC: 3453 AN: 10556

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22151 AN: 67964

Other (OTH) AF: 0.247 AC: 520 AN: 2106

Alfa AF: 0.308 Hom.: 12711

Bravo AF: 0.260

Asia WGS AF: 0.197 AC: 688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.42
DANN	Benign	0.82
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs1033540; hg19: chr6-131737302;