rs2075120

Variant names:

• chr22-16845542-C-T
• rs2075120
• ENST00000637740.1:n.340-377C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000637740.1(ENSG00000283535):​n.340-377C>T variant causes a intron 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: ENSG00000283535 ENST00000637740.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30
• Publications: 15 publications found

Genes affected

ENSG00000283535 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283535	ENST00000637740.1	n.340-377C>T		intron_variant	Intron 2 of 3	6

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

African (AFR) AF: 0.0417 AC: 1724 AN: 41358

American (AMR) AF: 0.198 AC: 3029 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 863 AN: 3468

East Asian (EAS) AF: 0.212 AC: 1091 AN: 5136

South Asian (SAS) AF: 0.243 AC: 1168 AN: 4798

European-Finnish (FIN) AF: 0.177 AC: 1871 AN: 10554

Middle Eastern (MID) AF: 0.269 AC: 78 AN: 290

European-Non Finnish (NFE) AF: 0.234 AC: 15881 AN: 67906

Other (OTH) AF: 0.189 AC: 399 AN: 2110

Alfa AF: 0.217 Hom.: 12506

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
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs2075120; hg19: chr22-17326432;