rs17061327

Variant names:

• chr5-163220501-T-C
• rs17061327
• ENST00000503504.2:n.512+36350A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-163220501-T-C
• chr5-163220501-T-G

Variant summary

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

The ENST00000509211.2(ENSG00000254186):​n.527+36350A>G variant causes a intron 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: ENSG00000254186 ENST00000509211.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 1 publications found

Genes affected

ENSG00000254186 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000509211.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000254186	ENST00000503504.2	TSL:5	n.512+36350A>G		intron	N/A
	ENSG00000254186	ENST00000509211.2	TSL:3	n.527+36350A>G		intron	N/A
	ENSG00000254186	ENST00000646617.1		n.323-131155A>G		intron	N/A

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

African (AFR) AF: 0.100 AC: 4169 AN: 41526

American (AMR) AF: 0.189 AC: 2889 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0995 AC: 345 AN: 3466

East Asian (EAS) AF: 0.510 AC: 2632 AN: 5162

South Asian (SAS) AF: 0.237 AC: 1145 AN: 4832

European-Finnish (FIN) AF: 0.0980 AC: 1037 AN: 10580

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0703 AC: 4780 AN: 68022

Other (OTH) AF: 0.123 AC: 259 AN: 2114

Alfa AF: 0.0899 Hom.: 2763

Bravo AF: 0.122

Asia WGS AF: 0.319 AC: 1108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.66
DANN	Benign	0.41
PhyloP100		-1.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17061327;

hg19: chr5-162647507;