rs4639966

Variant names:

• chr11-118702810-T-C
• rs4639966
• ENST00000646572.2:n.230-1798T>C

Variant summary

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

The ENST00000646572.2(ENSG00000255422):​n.230-1798T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,162 control chromosomes in the GnomAD database, including 4,328 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 0.24 (4328 hom., cov: 33)
• Consequence: ENSG00000255422 ENST00000646572.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.244
• Publications: 48 publications found

Genes affected

ENSG00000255422 (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 = 0.34 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000646572.2. 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
	ENSG00000255422	ENST00000646572.2		n.230-1798T>C		intron	N/A
	ENSG00000255422	ENST00000702882.1		n.230-1869T>C		intron	N/A
	ENSG00000255422	ENST00000775653.1		n.230+2167T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35775 AN: 152044 Hom.: 4325 Cov.: 33

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.235 AC: 35795 AN: 152162 Hom.: 4328 Cov.: 33 AF XY: 0.235 AC XY: 17488 AN XY: 74384

African (AFR) AF: 0.218 AC: 9049 AN: 41514

American (AMR) AF: 0.176 AC: 2685 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 892 AN: 3472

East Asian (EAS) AF: 0.353 AC: 1830 AN: 5180

South Asian (SAS) AF: 0.320 AC: 1541 AN: 4818

European-Finnish (FIN) AF: 0.258 AC: 2728 AN: 10582

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16312 AN: 68000

Other (OTH) AF: 0.245 AC: 517 AN: 2114

Alfa AF: 0.238 Hom.: 13565

Bravo AF: 0.226

Asia WGS AF: 0.332 AC: 1154 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	7.0
DANN	Benign	0.68
PhyloP100		-0.24

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: rs4639966;

hg19: chr11-118573519;