rs4620729

Variant names:

• chr11-69212868-C-A
• rs4620729
• ENST00000779509.1:n.138+16686C>A

Variant summary

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

The ENST00000779509.1(ENSG00000301530):​n.138+16686C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 152,088 control chromosomes in the GnomAD database, including 21,916 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 0.52 (21916 hom., cov: 33)
• Consequence: ENSG00000301530 ENST00000779509.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.258
• Publications: 15 publications found

Genes affected

ENSG00000301530 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.667 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
ENSG00000301530	ENST00000779509.1	n.138+16686C>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78943 AN: 151970 Hom.: 21872 Cov.: 33

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.0664

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.520 AC: 79039 AN: 152088 Hom.: 21916 Cov.: 33 AF XY: 0.512 AC XY: 38030 AN XY: 74346

African (AFR) AF: 0.673 AC: 27935 AN: 41498

American (AMR) AF: 0.392 AC: 5990 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2310 AN: 3470

East Asian (EAS) AF: 0.0655 AC: 339 AN: 5172

South Asian (SAS) AF: 0.329 AC: 1587 AN: 4818

European-Finnish (FIN) AF: 0.468 AC: 4952 AN: 10578

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34230 AN: 67948

Other (OTH) AF: 0.534 AC: 1128 AN: 2112

Alfa AF: 0.516 Hom.: 9460

Bravo AF: 0.524

Asia WGS AF: 0.297 AC: 1032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.82
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs4620729; hg19: chr11-68980335;