17-50631711-T-C

Variant names:

• chr17-50631711-T-C
• rs2214566
• ENST00000502435.2:n.238+29A>G

Variant summary

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

The ENST00000502435.2(ENSG00000251239):​n.238+29A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.786 in 152,302 control chromosomes in the GnomAD database, including 47,885 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 0.79 (47848 hom., cov: 33)
  • Exomes 𝑓: 0.72 (37 hom.)
• Consequence: ENSG00000251239 ENST00000502435.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16
• Publications: 1 publications found

Genes affected

ENSG00000251239 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000502435.2. 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
	ENSG00000251239	ENST00000502435.2	TSL:2	n.238+29A>G		intron	N/A
	ENSG00000251239	ENST00000746096.1		n.190-4371A>G		intron	N/A
	ENSG00000297214	ENST00000746227.1		n.-73T>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.786 AC: 119466 AN: 152046 Hom.: 47791 Cov.: 33

Gnomad AFR AF: 0.916

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.787

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.736

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.758

GnomAD4 exome AF: 0.725 AC: 100 AN: 138 Hom.: 37 Cov.: 0 AF XY: 0.730 AC XY: 73 AN XY: 100

African (AFR) AF: 1.00 AC: 6 AN: 6

American (AMR) AF: 0.750 AC: 3 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 6 AN: 6

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.500 AC: 5 AN: 10

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.740 AC: 74 AN: 100

Other (OTH) AF: 0.500 AC: 5 AN: 10

GnomAD4 genome AF: 0.786 AC: 119584 AN: 152164 Hom.: 47848 Cov.: 33 AF XY: 0.792 AC XY: 58935 AN XY: 74384

African (AFR) AF: 0.916 AC: 38047 AN: 41542

American (AMR) AF: 0.788 AC: 12047 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.730 AC: 2535 AN: 3472

East Asian (EAS) AF: 0.996 AC: 5131 AN: 5150

South Asian (SAS) AF: 0.853 AC: 4120 AN: 4828

European-Finnish (FIN) AF: 0.762 AC: 8068 AN: 10582

Middle Eastern (MID) AF: 0.740 AC: 216 AN: 292

European-Non Finnish (NFE) AF: 0.692 AC: 47070 AN: 67986

Other (OTH) AF: 0.761 AC: 1606 AN: 2110

Alfa AF: 0.791 Hom.: 24510

Bravo AF: 0.795

Asia WGS AF: 0.936 AC: 3257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	18
DANN	Benign	0.85
PhyloP100		1.2

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: rs2214566;

hg19: chr17-48709072;