rs4929966

Variant names:

• chr11-2176206-C-G
• rs4929966
• ENST00000729780.1:n.203-1312G>C

Variant summary

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

The ENST00000729780.1(ENSG00000295395):​n.203-1312G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,178 control chromosomes in the GnomAD database, including 3,460 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 0.19 (3460 hom., cov: 34)
• Consequence: ENSG00000295395 ENST00000729780.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 10 publications found

Genes affected

ENSG00000295395 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295395	ENST00000729780.1	n.203-1312G>C		intron_variant	Intron 1 of 2
ENSG00000295395	ENST00000729781.1	n.227-1312G>C		intron_variant	Intron 1 of 2
ENSG00000295395	ENST00000729782.1	n.196-853G>C		intron_variant	Intron 1 of 3
ENSG00000295395	ENST00000729783.1	n.156-1312G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28779 AN: 152060 Hom.: 3458 Cov.: 34

Gnomad AFR AF: 0.0538

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.0441

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.189 AC: 28785 AN: 152178 Hom.: 3460 Cov.: 34 AF XY: 0.186 AC XY: 13835 AN XY: 74394

African (AFR) AF: 0.0536 AC: 2227 AN: 41534

American (AMR) AF: 0.217 AC: 3312 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 792 AN: 3470

East Asian (EAS) AF: 0.0440 AC: 228 AN: 5176

South Asian (SAS) AF: 0.135 AC: 652 AN: 4832

European-Finnish (FIN) AF: 0.228 AC: 2415 AN: 10604

Middle Eastern (MID) AF: 0.0993 AC: 29 AN: 292

European-Non Finnish (NFE) AF: 0.272 AC: 18513 AN: 67954

Other (OTH) AF: 0.158 AC: 333 AN: 2114

Alfa AF: 0.226 Hom.: 557

Bravo AF: 0.183

Asia WGS AF: 0.0960 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.41
DANN	Benign	0.39
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs4929966; hg19: chr11-2197436;