rs686339

Positions:

• chr12-52630028-G-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

KRT73 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KRT73	XM_047428761.1	c.-11295-209C>T		intron_variant			XP_047284717.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.285

Alfa AF: 0.270 Hom.: 2577

Bravo AF: 0.311

Asia WGS AF: 0.314 AC: 1091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs686339; hg19: chr12-53023812;