rs7569716

chr2-22345841-A-T

Variant summary

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

The ENST00000450551.1(ENSG00000228999):n.71-134847T>A 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 0.207 in 149,192 control chromosomes in the GnomAD database, including 4,055 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 0.21 (4055 hom., cov: 33)
• Consequence: ENST00000450551.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06

Genes affected

(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 (AFR) allele frequency at 95% confidence interval = 0.376 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
	ENST00000450551.1	n.71-134847T>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.207 AC: 30905 AN: 149100 Hom.: 4047 Cov.: 33

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.260

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.207 AC: 30945 AN: 149192 Hom.: 4055 Cov.: 33 AF XY: 0.208 AC XY: 15191 AN XY: 72962

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.213

Alfa AF: 0.167 Hom.: 362

Bravo AF: 0.220

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	12
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7569716; hg19: chr2-22568713;