rs7561569

Variant names:

• chr2-191154820-C-A
• rs7561569
• ENST00000623836.1:n.1251G>T

Variant summary

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

The ENST00000623836.1(ENSG00000280083):​n.1251G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 150,134 control chromosomes in the GnomAD database, including 23,069 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 (23067 hom., cov: 33)
  • Exomes 𝑓: 0.36 (2 hom.)
• Consequence: ENSG00000280083 ENST00000623836.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204

Genes affected

ENSG00000280083 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.666 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
ENSG00000280083	ENST00000623836.1	n.1251G>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.514 AC: 77089 AN: 149994 Hom.: 23067 Cov.: 33

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.526

GnomAD4 exome AF: 0.357 AC: 10 AN: 28 Hom.: 2 Cov.: 0 AF XY: 0.385 AC XY: 10 AN XY: 26

Gnomad4 AFR exome AF: 0.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 NFE exome AF: 0.333

GnomAD4 genome AF: 0.514 AC: 77100 AN: 150106 Hom.: 23067 Cov.: 33 AF XY: 0.521 AC XY: 38189 AN XY: 73350

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.639

Gnomad4 ASJ AF: 0.640

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.685

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.641

Gnomad4 OTH AF: 0.523

Alfa AF: 0.538 Hom.: 3596

Bravo AF: 0.497

Asia WGS AF: 0.525 AC: 1821 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7561569; hg19: chr2-192019546;