rs6755560

Variant names:

• chr2-206853059-T-C
• rs6755560
• ENST00000438070.3:n.347+9847T>C

Variant summary

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

The ENST00000438070.3(ENSG00000229321):​n.347+9847T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 151,686 control chromosomes in the GnomAD database, including 5,559 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 0.26 (5559 hom., cov: 31)
• Consequence: ENSG00000229321 ENST00000438070.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583
• Publications: 7 publications found

Genes affected

ENSG00000229321 (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 (NFE) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000438070.3. 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
	ENSG00000229321	ENST00000438070.3	TSL:3	n.347+9847T>C		intron	N/A
	ENSG00000229321	ENST00000658291.1		n.3035-10337T>C		intron	N/A
	ENSG00000229321	ENST00000658889.1		n.2974-26324T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39639 AN: 151568 Hom.: 5555 Cov.: 31

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.0297

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.261 AC: 39656 AN: 151686 Hom.: 5559 Cov.: 31 AF XY: 0.259 AC XY: 19202 AN XY: 74102

African (AFR) AF: 0.188 AC: 7761 AN: 41342

American (AMR) AF: 0.304 AC: 4632 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1115 AN: 3468

East Asian (EAS) AF: 0.0295 AC: 152 AN: 5146

South Asian (SAS) AF: 0.191 AC: 910 AN: 4774

European-Finnish (FIN) AF: 0.272 AC: 2859 AN: 10522

Middle Eastern (MID) AF: 0.253 AC: 74 AN: 292

European-Non Finnish (NFE) AF: 0.314 AC: 21323 AN: 67880

Other (OTH) AF: 0.266 AC: 559 AN: 2104

Alfa AF: 0.283 Hom.: 11046

Bravo AF: 0.258

Asia WGS AF: 0.120 AC: 420 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	4.5
DANN	Benign	0.69
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs6755560; hg19: chr2-207717783;