rs4980785

Variant names:

• chr11-69419726-C-T
• rs4980785
• ENST00000728815.1:n.819+71G>A

Variant summary

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

The ENST00000728815.1(ENSG00000295246):​n.819+71G>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 152,078 control chromosomes in the GnomAD database, including 22,119 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 (22119 hom., cov: 33)
• Consequence: ENSG00000295246 ENST00000728815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480
• Publications: 20 publications found

Genes affected

ENSG00000295246 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.727 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
ENSG00000295246	ENST00000728815.1	n.819+71G>A		intron_variant	Intron 1 of 1
ENSG00000295246	ENST00000728816.1	n.299+71G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78939 AN: 151960 Hom.: 22061 Cov.: 33

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.520 AC: 79066 AN: 152078 Hom.: 22119 Cov.: 33 AF XY: 0.518 AC XY: 38532 AN XY: 74348

African (AFR) AF: 0.734 AC: 30433 AN: 41490

American (AMR) AF: 0.550 AC: 8403 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1214 AN: 3472

East Asian (EAS) AF: 0.510 AC: 2634 AN: 5168

South Asian (SAS) AF: 0.352 AC: 1696 AN: 4824

European-Finnish (FIN) AF: 0.446 AC: 4713 AN: 10564

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.418 AC: 28398 AN: 67956

Other (OTH) AF: 0.467 AC: 986 AN: 2112

Alfa AF: 0.450 Hom.: 38445

Bravo AF: 0.537

Asia WGS AF: 0.470 AC: 1636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.2
DANN	Benign	0.75
PhyloP100		-0.048

Splicing

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

Other links and lift over

dbSNP: rs4980785; hg19: chr11-69234494;