rs1592778

chr5-163393889-G-A

Variant summary

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

The ENST00000646617.1(ENSG00000254186):n.322+31914C>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 0.139 in 151,944 control chromosomes in the GnomAD database, including 1,529 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 0.14 (1529 hom., cov: 32)
• Consequence: ENST00000646617.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.307

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377700	XR_001742961.2	n.1236+18430C>T		intron_variant, non_coding_transcript_variant
LOC105377700	XR_001742965.1	n.1236+18430C>T		intron_variant, non_coding_transcript_variant
LOC105377700	XR_002956233.2	n.1236+18430C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000646617.1	n.322+31914C>T		intron_variant, non_coding_transcript_variant
	ENST00000503504.1	n.355+31914C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21073 AN: 151826 Hom.: 1529 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.0993

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.0192

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.139 AC: 21070 AN: 151944 Hom.: 1529 Cov.: 32 AF XY: 0.141 AC XY: 10453 AN XY: 74266

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.0991

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.0191

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.125

Alfa AF: 0.143 Hom.: 206

Bravo AF: 0.131

Asia WGS AF: 0.108 AC: 376 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.5
Dann	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1592778; hg19: chr5-162820895;