rs686339

Variant names:

• chr12-52630028-G-A
• rs686339
• XM_047428761.1:c.-11295-209C>T

Variant summary

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

The XM_047428761.1(KRT73):​c.-11295-209C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 151,934 control chromosomes in the GnomAD database, including 7,559 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 (7559 hom., cov: 31)
• Consequence: KRT73 XM_047428761.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 11 publications found

Genes affected

KRT73 (HGNC:28928): (keratin 73) Keratins are intermediate filament proteins responsible for the structural integrity of epithelial cells and are subdivided into epithelial keratins and hair keratins. This gene encodes a protein that is expressed in the inner root sheath of hair follicles. The type II keratins are clustered in a region of chromosome 12q13.[provided by RefSeq, Jun 2009]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46592 AN: 151816 Hom.: 7550 Cov.: 31

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.307 AC: 46634 AN: 151934 Hom.: 7559 Cov.: 31 AF XY: 0.308 AC XY: 22865 AN XY: 74260

African (AFR) AF: 0.398 AC: 16464 AN: 41414

American (AMR) AF: 0.318 AC: 4854 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 758 AN: 3470

East Asian (EAS) AF: 0.266 AC: 1375 AN: 5166

South Asian (SAS) AF: 0.331 AC: 1588 AN: 4802

European-Finnish (FIN) AF: 0.298 AC: 3145 AN: 10568

Middle Eastern (MID) AF: 0.202 AC: 59 AN: 292

European-Non Finnish (NFE) AF: 0.256 AC: 17380 AN: 67930

Other (OTH) AF: 0.285 AC: 601 AN: 2106

Alfa AF: 0.270 Hom.: 2905

Bravo AF: 0.311

Asia WGS AF: 0.314 AC: 1091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.65
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs686339; hg19: chr12-53023812;