5-163225545-C-T

Position:

• chr5-163225545-C-T

Variant summary

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

The ENST00000646617.1(ENSG00000254186):​n.323-136199G>A 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 0.389 in 151,840 control chromosomes in the GnomAD database, including 16,519 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 0.39 (16519 hom., cov: 32)
• Consequence: ENST00000646617.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377700	XR_001742961.2	n.1373+31306G>A		intron_variant, non_coding_transcript_variant
LOC105377700	XR_002956233.2	n.1374-14698G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000646617.1	n.323-136199G>A		intron_variant, non_coding_transcript_variant
	ENST00000509211.1	n.117+31306G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59006 AN: 151722 Hom.: 16482 Cov.: 32

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.389 AC: 59097 AN: 151840 Hom.: 16519 Cov.: 32 AF XY: 0.388 AC XY: 28776 AN XY: 74216

Gnomad4 AFR AF: 0.787

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.403

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.371

Alfa AF: 0.221 Hom.: 3929

Bravo AF: 0.414

Asia WGS AF: 0.437 AC: 1519 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4448013; hg19: chr5-162652551;