2-56172199-C-T

Variant names:

• chr2-56172199-C-T
• rs4672095
• ENST00000606639.1:n.465+2004C>T

Variant summary

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

The ENST00000606639.1(ENSG00000272180):​n.465+2004C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 152,020 control chromosomes in the GnomAD database, including 16,149 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 0.45 (16149 hom., cov: 32)
• Consequence: ENSG00000272180 ENST00000606639.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 7 publications found

Genes affected

ENSG00000272180 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374690	XR_940109.3	n.1165+2004C>T		intron_variant	Intron 8 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000272180	ENST00000606639.1	n.465+2004C>T		intron_variant	Intron 4 of 6	1
ENSG00000271894	ENST00000607540.2	n.396+2004C>T		intron_variant	Intron 3 of 4	5
ENSG00000272180	ENST00000717252.1	n.288-8924C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.454 AC: 69026 AN: 151902 Hom.: 16132 Cov.: 32

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.455 AC: 69094 AN: 152020 Hom.: 16149 Cov.: 32 AF XY: 0.449 AC XY: 33331 AN XY: 74306

African (AFR) AF: 0.551 AC: 22829 AN: 41442

American (AMR) AF: 0.464 AC: 7083 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1808 AN: 3470

East Asian (EAS) AF: 0.256 AC: 1323 AN: 5176

South Asian (SAS) AF: 0.286 AC: 1379 AN: 4822

European-Finnish (FIN) AF: 0.414 AC: 4376 AN: 10572

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28824 AN: 67950

Other (OTH) AF: 0.456 AC: 965 AN: 2114

Alfa AF: 0.433 Hom.: 25251

Bravo AF: 0.469

Asia WGS AF: 0.263 AC: 916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.15
DANN	Benign	0.58
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4672095; hg19: chr2-56399334;