rs1033540

chr6-131416162-C-T

Variant summary

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

The ENST00000702750.1(ENSG00000290067):n.282+23968G>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 0.271 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: ENST00000702750.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105378005	XR_001744344.2	n.275+23968G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000702750.1	n.282+23968G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.247

Alfa AF: 0.314 Hom.: 10332

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1033540; hg19: chr6-131737302;