2-64726875-G-A

Variant names:

• chr2-64726875-G-A
• rs7560607
• ENST00000476805.2:n.725+23406C>T

Variant summary

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

The ENST00000476805.2(SERTAD2):​n.725+23406C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.888 in 152,240 control chromosomes in the GnomAD database, including 60,731 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 0.89 (60731 hom., cov: 31)
• Consequence: SERTAD2 ENST00000476805.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.785
• Publications: 1 publications found

Genes affected

SERTAD2 (HGNC:30784): (SERTA domain containing 2) Predicted to enable transcription coactivator activity. Acts upstream of or within negative regulation of cell growth. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.943 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000476805.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SERTAD2	ENST00000476805.2	TSL:3	n.725+23406C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.889 AC: 135172 AN: 152122 Hom.: 60718 Cov.: 31

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.952

Gnomad AMR AF: 0.925

Gnomad ASJ AF: 0.887

Gnomad EAS AF: 0.935

Gnomad SAS AF: 0.879

Gnomad FIN AF: 0.987

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.949

Gnomad OTH AF: 0.887

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

GnomAD4 genome AF: 0.888 AC: 135229 AN: 152240 Hom.: 60731 Cov.: 31 AF XY: 0.890 AC XY: 66281 AN XY: 74454

African (AFR) AF: 0.744 AC: 30860 AN: 41490

American (AMR) AF: 0.925 AC: 14147 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.887 AC: 3078 AN: 3470

East Asian (EAS) AF: 0.936 AC: 4852 AN: 5186

South Asian (SAS) AF: 0.878 AC: 4243 AN: 4832

European-Finnish (FIN) AF: 0.987 AC: 10481 AN: 10620

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.949 AC: 64574 AN: 68022

Other (OTH) AF: 0.887 AC: 1876 AN: 2114

Alfa AF: 0.912 Hom.: 8222

Bravo AF: 0.878

Asia WGS AF: 0.902 AC: 3139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	6.1
DANN	Benign	0.75
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs7560607; hg19: chr2-64954009;