NM_033032.3:c.240C>T

Variant names:

• chr17-41054972-G-A
• rs1375582289
• NM_033032.3:c.240C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_033032.3(KRTAP2-2):​c.240C>T​(p.Cys80Cys) variant causes a synonymous change. 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 0.0000090 (0 hom., cov: 14)
  • Exomes 𝑓: 9.8e-7 (0 hom.)
• Consequence: KRTAP2-2 NM_033032.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.81
• Publications: 0 publications found

Genes affected

KRTAP2-2 (HGNC:18905): (keratin associated protein 2-2) Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000306126 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033032.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KRTAP2-2	NM_033032.3	MANE Select	c.240C>T	p.Cys80Cys	synonymous	Exon 1 of 1	NP_149021.2	Q9BYT5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KRTAP2-2	ENST00000398477.1	TSL:6 MANE Select	c.240C>T	p.Cys80Cys	synonymous	Exon 1 of 1	ENSP00000381494.1	Q9BYT5
	ENSG00000306126	ENST00000815517.1		n.220-5327G>A		intron	N/A
	ENSG00000306126	ENST00000815518.1		n.160-5327G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00000901 AC: 1 AN: 110942 Hom.: 0 Cov.: 14

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.000713

GnomAD4 exome AF: 9.79e-7 AC: 1 AN: 1021162 Hom.: 0 Cov.: 17 AF XY: 0.00000197 AC XY: 1 AN XY: 507548

African (AFR) AF: 0.00 AC: 0 AN: 24864

American (AMR) AF: 0.00 AC: 0 AN: 28668

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19152

East Asian (EAS) AF: 0.00 AC: 0 AN: 34638

South Asian (SAS) AF: 0.00 AC: 0 AN: 66202

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 30620

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3282

European-Non Finnish (NFE) AF: 0.00000130 AC: 1 AN: 768018

Other (OTH) AF: 0.00 AC: 0 AN: 45718

GnomAD4 genome AF: 0.00000901 AC: 1 AN: 111026 Hom.: 0 Cov.: 14 AF XY: 0.0000193 AC XY: 1 AN XY: 51724

African (AFR) AF: 0.00 AC: 0 AN: 28576

American (AMR) AF: 0.00 AC: 0 AN: 10672

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2834

East Asian (EAS) AF: 0.00 AC: 0 AN: 4598

South Asian (SAS) AF: 0.00 AC: 0 AN: 3276

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6366

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 264

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 52310

Other (OTH) AF: 0.000705 AC: 1 AN: 1418

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	12
DANN	Benign	0.92
PhyloP100		3.8
PromoterAI		0.0043	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1375582289; hg19: chr17-39211224;