rs2075120

chr22-16845542-C-T

Variant summary

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

The ENST00000637740.1(ENSG00000283535):n.340-377C>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 0.174 in 151,802 control chromosomes in the GnomAD database, including 2,848 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 0.17 (2848 hom., cov: 32)
• Consequence: ENST00000637740.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.232 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
	ENST00000637740.1	n.340-377C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26351 AN: 151686 Hom.: 2848 Cov.: 32

Gnomad AFR AF: 0.0418

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.174 AC: 26357 AN: 151802 Hom.: 2848 Cov.: 32 AF XY: 0.174 AC XY: 12942 AN XY: 74202

Gnomad4 AFR AF: 0.0417

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.189

Alfa AF: 0.229 Hom.: 8486

Bravo AF: 0.169

Asia WGS AF: 0.214 AC: 745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.6
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2075120; hg19: chr22-17326432;