chr5-169472983-T-C

Variant names:

• chr5-169472983-T-C
• rs13156607
• ENST00000827138.1:n.300-1442T>C

Variant summary

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

The ENST00000827138.1(ENSG00000307563):​n.300-1442T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 152,046 control chromosomes in the GnomAD database, including 32,730 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 0.65 (32730 hom., cov: 32)
• Consequence: ENSG00000307563 ENST00000827138.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 11 publications found

Genes affected

ENSG00000307563 (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 (EAS) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377714	XR_941200.3	n.461-13047A>G		intron_variant	Intron 2 of 2
LOC105377715	XR_941204.3	n.241-1442T>C		intron_variant	Intron 2 of 3
LOC105377715	XR_941205.3	n.230+3743T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307563	ENST00000827138.1	n.300-1442T>C		intron_variant	Intron 2 of 4
ENSG00000307563	ENST00000827139.1	n.248+3743T>C		intron_variant	Intron 2 of 3
ENSG00000307563	ENST00000827140.1	n.264-1442T>C		intron_variant	Intron 2 of 4
ENSG00000307563	ENST00000827141.1	n.269-1442T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98954 AN: 151928 Hom.: 32698 Cov.: 32

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.971

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.651 AC: 99039 AN: 152046 Hom.: 32730 Cov.: 32 AF XY: 0.655 AC XY: 48662 AN XY: 74328

African (AFR) AF: 0.616 AC: 25558 AN: 41460

American (AMR) AF: 0.749 AC: 11432 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2214 AN: 3470

East Asian (EAS) AF: 0.971 AC: 5026 AN: 5176

South Asian (SAS) AF: 0.671 AC: 3235 AN: 4818

European-Finnish (FIN) AF: 0.574 AC: 6070 AN: 10570

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.636 AC: 43238 AN: 67970

Other (OTH) AF: 0.664 AC: 1400 AN: 2110

Alfa AF: 0.651 Hom.: 122792

Bravo AF: 0.664

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.38
DANN	Benign	0.41
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs13156607; hg19: chr5-168899987;