rs7560607

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr2-64726875-G-A
• chr2-64726875-G-C
• chr2-64726875-G-T

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 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

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SERTAD2	ENST00000476805.2	n.725+23406C>T		intron_variant	Intron 1 of 1	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;