rs17061327

chr5-163220501-T-Cchr5-163220501-T-G

Variant summary

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

The ENST00000646617.1(ENSG00000254186):n.323-131155A>G 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 0.114 in 152,188 control chromosomes in the GnomAD database, including 1,594 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 (1594 hom., cov: 32)
• Consequence: ENST00000646617.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377700	XR_001742961.2	n.1373+36350A>G		intron_variant, non_coding_transcript_variant
LOC105377700	XR_002956233.2	n.1374-9654A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000646617.1	n.323-131155A>G		intron_variant, non_coding_transcript_variant
	ENST00000509211.1	n.117+36350A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17359 AN: 152070 Hom.: 1586 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.0995

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.0980

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0703

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.114 AC: 17389 AN: 152188 Hom.: 1594 Cov.: 32 AF XY: 0.122 AC XY: 9099 AN XY: 74400

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.0995

Gnomad4 EAS AF: 0.510

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.0980

Gnomad4 NFE AF: 0.0703

Gnomad4 OTH AF: 0.123

Alfa AF: 0.0877 Hom.: 1834

Bravo AF: 0.122

Asia WGS AF: 0.319 AC: 1108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.66
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17061327; hg19: chr5-162647507;