6-131416162-C-T

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000702750.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290067	ENST00000702750.2		n.303+23968G>A		intron	N/A
	ENSG00000290067	ENST00000771190.1		n.292+23968G>A		intron	N/A
	ENSG00000290067	ENST00000771191.1		n.298+23968G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1033540;

hg19: chr6-131737302;