ENST00000839999.1:n.282+31106G>A

Variant names:

• chr20-7771719-C-T
• rs6077251
• ENST00000839999.1:n.282+31106G>A

Variant summary

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

The ENST00000839999.1(ENSG00000309276):​n.282+31106G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 151,858 control chromosomes in the GnomAD database, including 1,536 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 0.12 (1536 hom., cov: 32)
• Consequence: ENSG00000309276 ENST00000839999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 9 publications found

Genes affected

ENSG00000309276 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.295 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
ENSG00000309276	ENST00000839999.1	n.282+31106G>A		intron_variant	Intron 1 of 4
ENSG00000309276	ENST00000840001.1	n.320-425G>A		intron_variant	Intron 1 of 1
ENSG00000309276	ENST00000840002.1	n.86-425G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18923 AN: 151742 Hom.: 1527 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.0615

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0896

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.125 AC: 18955 AN: 151858 Hom.: 1536 Cov.: 32 AF XY: 0.127 AC XY: 9392 AN XY: 74198

African (AFR) AF: 0.156 AC: 6482 AN: 41488

American (AMR) AF: 0.168 AC: 2520 AN: 15024

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 549 AN: 3464

East Asian (EAS) AF: 0.147 AC: 761 AN: 5170

South Asian (SAS) AF: 0.308 AC: 1485 AN: 4816

European-Finnish (FIN) AF: 0.0615 AC: 652 AN: 10596

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0896 AC: 6095 AN: 67996

Other (OTH) AF: 0.148 AC: 311 AN: 2098

Alfa AF: 0.105 Hom.: 4352

Bravo AF: 0.133

Asia WGS AF: 0.261 AC: 905 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.26
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs6077251; hg19: chr20-7752366;