rs2056169

Variant names:

• chr5-71763885-A-C
• rs2056169
• ENST00000728946.1:n.233+18287A>C

Your query was ambiguous. Multiple possible variants found:

• chr5-71763885-A-C
• chr5-71763885-A-G
• chr5-71763885-A-T

Variant summary

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

The ENST00000728946.1(ENSG00000295276):​n.233+18287A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 152,048 control chromosomes in the GnomAD database, including 9,656 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 0.32 (9656 hom., cov: 32)
• Consequence: ENSG00000295276 ENST00000728946.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.68
• Publications: 1 publications found

Genes affected

ENSG00000295276 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 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
ENSG00000295276	ENST00000728946.1	n.233+18287A>C		intron_variant	Intron 2 of 2
ENSG00000295276	ENST00000728947.1	n.119-12784A>C		intron_variant	Intron 1 of 3
ENSG00000295276	ENST00000728948.1	n.76+13812A>C		intron_variant	Intron 1 of 1
ENSG00000295276	ENST00000728949.1	n.58-12784A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48849 AN: 151930 Hom.: 9628 Cov.: 32

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.322 AC: 48937 AN: 152048 Hom.: 9656 Cov.: 32 AF XY: 0.321 AC XY: 23886 AN XY: 74326

African (AFR) AF: 0.562 AC: 23275 AN: 41446

American (AMR) AF: 0.292 AC: 4457 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 833 AN: 3466

East Asian (EAS) AF: 0.308 AC: 1592 AN: 5170

South Asian (SAS) AF: 0.317 AC: 1527 AN: 4818

European-Finnish (FIN) AF: 0.238 AC: 2520 AN: 10572

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13746 AN: 67988

Other (OTH) AF: 0.291 AC: 614 AN: 2112

Alfa AF: 0.204 Hom.: 2041

Bravo AF: 0.339

Asia WGS AF: 0.349 AC: 1212 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.035
DANN	Benign	0.42
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs2056169; hg19: chr5-71059712; COSMIC: COSV50461023;