rs626758

Variant names:

• chr12-52632782-T-C
• rs626758
• ENST00000550729.2:n.663+84A>G

Variant summary

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

The ENST00000550729.2(KRT128P):​n.663+84A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,616 control chromosomes in the GnomAD database, including 7,758 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 0.31 (7740 hom., cov: 33)
  • Exomes 𝑓: 0.31 (18 hom.)
• Consequence: KRT128P ENST00000550729.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.512
• Publications: 5 publications found

Genes affected

KRT128P (HGNC:48882): (keratin 128, pseudogene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000550729.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KRT128P	ENST00000550729.2	TSL:6	n.663+84A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.309 AC: 47040 AN: 152044 Hom.: 7731 Cov.: 33

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.284

GnomAD4 exome AF: 0.313 AC: 142 AN: 454 Hom.: 18 AF XY: 0.333 AC XY: 92 AN XY: 276

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.299 AC: 125 AN: 418

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.500 AC: 12 AN: 24

Other (OTH) AF: 0.250 AC: 1 AN: 4

GnomAD4 genome AF: 0.309 AC: 47082 AN: 152162 Hom.: 7740 Cov.: 33 AF XY: 0.311 AC XY: 23107 AN XY: 74404

African (AFR) AF: 0.411 AC: 17068 AN: 41484

American (AMR) AF: 0.319 AC: 4885 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 759 AN: 3472

East Asian (EAS) AF: 0.224 AC: 1161 AN: 5180

South Asian (SAS) AF: 0.329 AC: 1583 AN: 4816

European-Finnish (FIN) AF: 0.298 AC: 3159 AN: 10598

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17394 AN: 67994

Other (OTH) AF: 0.285 AC: 603 AN: 2114

Alfa AF: 0.286 Hom.: 763

Bravo AF: 0.314

Asia WGS AF: 0.299 AC: 1039 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.4
DANN	Benign	0.78
PhyloP100		-0.51

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs626758;

hg19: chr12-53026566;

COSMIC: COSV73574037;