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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369519	XR_001748408.2	n.113-1798T>C		intron_variant	Intron 1 of 2
LOC105369519	XR_007062909.1	n.252-1798T>C		intron_variant	Intron 2 of 3
LOC105369519	XR_007062910.1	n.206-1798T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255422	ENST00000646572.2	n.230-1798T>C		intron_variant	Intron 1 of 2
ENSG00000255422	ENST00000702882.1	n.230-1869T>C		intron_variant	Intron 1 of 2
ENSG00000255422	ENST00000775653.1	n.230+2167T>C		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs4639966; hg19: chr11-118573519;