rs2345144

Variant names:

• chr6-170505603-C-T
• rs2345144
• ENST00000722532.1:n.122-17097G>A

Variant summary

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

The ENST00000722532.1(ENSG00000294293):​n.122-17097G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,176 control chromosomes in the GnomAD database, including 7,656 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 0.31 (7656 hom., cov: 33)
• Consequence: ENSG00000294293 ENST00000722532.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100
• Publications: 4 publications found

Genes affected

ENSG00000294293 (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 (AFR) allele frequency at 95% confidence interval = 0.391 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
ENSG00000294293	ENST00000722532.1	n.122-17097G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47082 AN: 152058 Hom.: 7654 Cov.: 33

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.309 AC: 47096 AN: 152176 Hom.: 7656 Cov.: 33 AF XY: 0.306 AC XY: 22751 AN XY: 74394

African (AFR) AF: 0.396 AC: 16416 AN: 41500

American (AMR) AF: 0.262 AC: 4008 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 995 AN: 3470

East Asian (EAS) AF: 0.182 AC: 943 AN: 5184

South Asian (SAS) AF: 0.350 AC: 1691 AN: 4826

European-Finnish (FIN) AF: 0.237 AC: 2512 AN: 10588

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19592 AN: 68008

Other (OTH) AF: 0.287 AC: 606 AN: 2110

Alfa AF: 0.301 Hom.: 2046

Bravo AF: 0.309

Asia WGS AF: 0.238 AC: 828 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	1.3
DANN	Benign	0.48
PhyloP100		-0.010

Splicing

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

Other links and lift over

dbSNP: rs2345144; hg19: chr6-170814691;