12-22009035-G-T

Variant names:

• chr12-22009035-G-T
• rs16915844

Variant summary

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

The variant allele was found at a frequency of 0.196 in 152,122 control chromosomes in the GnomAD database, including 3,597 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 0.20 (3597 hom., cov: 32)
• Consequence: THEM4P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 3 publications found

Genes affected

THEM4P1 (HGNC:32692):

ENSG00000255627 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
THEM4P1		n.22009035G>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255627	ENST00000541534.1	n.*155G>T		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29772 AN: 152004 Hom.: 3591 Cov.: 32

Gnomad AFR AF: 0.0543

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.196 AC: 29780 AN: 152122 Hom.: 3597 Cov.: 32 AF XY: 0.194 AC XY: 14450 AN XY: 74368

African (AFR) AF: 0.0543 AC: 2254 AN: 41534

American (AMR) AF: 0.249 AC: 3805 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 949 AN: 3472

East Asian (EAS) AF: 0.314 AC: 1617 AN: 5152

South Asian (SAS) AF: 0.221 AC: 1062 AN: 4814

European-Finnish (FIN) AF: 0.165 AC: 1752 AN: 10596

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.259 AC: 17603 AN: 67960

Other (OTH) AF: 0.217 AC: 458 AN: 2108

Alfa AF: 0.202 Hom.: 1639

Bravo AF: 0.199

Asia WGS AF: 0.255 AC: 886 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	1.4
DANN	Benign	0.38
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs16915844; hg19: chr12-22161969; COSMIC: COSV73426433;