5-172766674-C-T

Position:

• chr5-172766674-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000523005.1(ENSG00000253736):​n.69+3626C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,226 control chromosomes in the GnomAD database, including 1,263 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 0.11 (1263 hom., cov: 33)
• Consequence: ENST00000523005.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.328

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000523005.1	n.69+3626C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16273 AN: 152112 Hom.: 1255 Cov.: 33

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0554

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0496

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0479

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.107 AC: 16314 AN: 152226 Hom.: 1263 Cov.: 33 AF XY: 0.109 AC XY: 8129 AN XY: 74436

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.0554

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.0496

Gnomad4 NFE AF: 0.0479

Gnomad4 OTH AF: 0.111

Alfa AF: 0.0681 Hom.: 133

Bravo AF: 0.120

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	14
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs881811; hg19: chr5-172193677;