2-47965823-G-C

Variant names:

• chr2-47965823-G-C
• rs6717617
• ENST00000447571.5:n.442-17414C>G

Variant summary

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

The ENST00000447571.5(ENSG00000230773):​n.442-17414C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.717 in 152,062 control chromosomes in the GnomAD database, including 40,303 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 0.72 (40303 hom., cov: 31)
• Consequence: ENSG00000230773 ENST00000447571.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.319
• Publications: 1 publications found

Genes affected

ENSG00000230773 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000447571.5. 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
	ENSG00000230773	ENST00000447571.5	TSL:1	n.442-17414C>G		intron	N/A
	ENSG00000230773	ENST00000587616.1	TSL:5	n.944-3247C>G		intron	N/A
	ENSG00000230773	ENST00000649883.1		n.403-17414C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108855 AN: 151944 Hom.: 40251 Cov.: 31

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.709

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

GnomAD4 genome AF: 0.717 AC: 108964 AN: 152062 Hom.: 40303 Cov.: 31 AF XY: 0.717 AC XY: 53287 AN XY: 74304

African (AFR) AF: 0.888 AC: 36877 AN: 41518

American (AMR) AF: 0.705 AC: 10767 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2405 AN: 3472

East Asian (EAS) AF: 0.934 AC: 4832 AN: 5176

South Asian (SAS) AF: 0.702 AC: 3380 AN: 4818

European-Finnish (FIN) AF: 0.583 AC: 6142 AN: 10542

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.622 AC: 42300 AN: 67954

Other (OTH) AF: 0.707 AC: 1490 AN: 2108

Alfa AF: 0.523 Hom.: 1328

Bravo AF: 0.736

Asia WGS AF: 0.824 AC: 2867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.77
DANN	Benign	0.54
PhyloP100		-0.32

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: rs6717617;

hg19: chr2-48192962;