chr2-64726875-G-A

Position:

• chr2-64726875-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000476805.2(SERTAD2):​n.725+23406C>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.785

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SERTAD2	ENST00000476805.2	n.725+23406C>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.744

Gnomad4 AMR AF: 0.925

Gnomad4 ASJ AF: 0.887

Gnomad4 EAS AF: 0.936

Gnomad4 SAS AF: 0.878

Gnomad4 FIN AF: 0.987

Gnomad4 NFE AF: 0.949

Gnomad4 OTH AF: 0.887

Alfa AF: 0.918 Hom.: 7995

Bravo AF: 0.878

Asia WGS AF: 0.902 AC: 3139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7560607; hg19: chr2-64954009;