7-20822683-C-T

Variant names:

• chr7-20822683-C-T
• rs2709736
• ENST00000773384.1:n.115-4635C>T

Variant summary

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

The ENST00000773384.1(ENSG00000300678):​n.115-4635C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 152,022 control chromosomes in the GnomAD database, including 20,557 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 0.51 (20557 hom., cov: 33)
• Consequence: ENSG00000300678 ENST00000773384.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163
• Publications: 16 publications found

Genes affected

ENSG00000300678 (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 (AFR) allele frequency at 95% confidence interval = 0.672 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
ENSG00000300678	ENST00000773384.1	n.115-4635C>T		intron_variant	Intron 1 of 1
ENSG00000300678	ENST00000773385.1	n.224-4635C>T		intron_variant	Intron 1 of 1
ENSG00000300678	ENST00000773386.1	n.190-3996C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.507 AC: 77060 AN: 151904 Hom.: 20521 Cov.: 33

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.508 AC: 77154 AN: 152022 Hom.: 20557 Cov.: 33 AF XY: 0.501 AC XY: 37200 AN XY: 74312

African (AFR) AF: 0.679 AC: 28158 AN: 41484

American (AMR) AF: 0.458 AC: 6991 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1557 AN: 3466

East Asian (EAS) AF: 0.377 AC: 1947 AN: 5170

South Asian (SAS) AF: 0.416 AC: 2005 AN: 4820

European-Finnish (FIN) AF: 0.381 AC: 4020 AN: 10564

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.453 AC: 30759 AN: 67942

Other (OTH) AF: 0.484 AC: 1024 AN: 2114

Alfa AF: 0.474 Hom.: 42095

Bravo AF: 0.522

Asia WGS AF: 0.388 AC: 1351 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	3.6
DANN	Benign	0.40
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs2709736; hg19: chr7-20862302;