chr5-172492650-C-T

Variant names:

• chr5-172492650-C-T
• rs55867206
• ENST00000660356.2:n.405+13046C>T

Variant summary

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

The ENST00000660356.2(ENSG00000287814):​n.405+13046C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0832 in 152,206 control chromosomes in the GnomAD database, including 660 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 0.083 (660 hom., cov: 32)
• Consequence: ENSG00000287814 ENST00000660356.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383
• Publications: 2 publications found

Genes affected

ENSG00000287814 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377727	XR_001742994.2	n.522+12517C>T		intron_variant	Intron 1 of 1
LOC105377727	XR_941225.3	n.554+13046C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287814	ENST00000660356.2	n.405+13046C>T		intron_variant	Intron 1 of 1
ENSG00000287814	ENST00000718805.1	n.423+13046C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0833 AC: 12668 AN: 152086 Hom.: 662 Cov.: 32

Gnomad AFR AF: 0.0348

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0615

Gnomad ASJ AF: 0.0765

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0903

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

GnomAD4 genome AF: 0.0832 AC: 12657 AN: 152206 Hom.: 660 Cov.: 32 AF XY: 0.0838 AC XY: 6234 AN XY: 74428

African (AFR) AF: 0.0346 AC: 1439 AN: 41564

American (AMR) AF: 0.0614 AC: 940 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0765 AC: 265 AN: 3464

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5182

South Asian (SAS) AF: 0.155 AC: 744 AN: 4814

European-Finnish (FIN) AF: 0.146 AC: 1549 AN: 10588

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7453 AN: 67972

Other (OTH) AF: 0.0913 AC: 193 AN: 2114

Alfa AF: 0.101 Hom.: 114

Bravo AF: 0.0726

Asia WGS AF: 0.0770 AC: 269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.54
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs55867206; hg19: chr5-171919654;