10-68260465-T-C

Variant names:

• chr10-68260465-T-C
• rs2120902

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 0.139 in 152,570 control chromosomes in the GnomAD database, including 1,966 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 0.14 (1961 hom., cov: 32)
  • Exomes 𝑓: 0.18 (5 hom.)
• Consequence: KRT19P4 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257
• Publications: 2 publications found

Genes affected

KRT19P4 (HGNC:45073): (keratin 19 pseudogene 4)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000443208.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KRT19P4	ENST00000443208.1	TSL:6	n.-92T>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21106 AN: 152056 Hom.: 1960 Cov.: 32

Gnomad AFR AF: 0.0314

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.143

GnomAD4 exome AF: 0.177 AC: 70 AN: 396 Hom.: 5 AF XY: 0.176 AC XY: 49 AN XY: 278

African (AFR) AF: 0.00 AC: 0 AN: 6

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 1 AN: 4

East Asian (EAS) AF: 0.143 AC: 2 AN: 14

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

European-Finnish (FIN) AF: 0.206 AC: 21 AN: 102

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.175 AC: 42 AN: 240

Other (OTH) AF: 0.0833 AC: 2 AN: 24

GnomAD4 genome AF: 0.139 AC: 21115 AN: 152174 Hom.: 1961 Cov.: 32 AF XY: 0.144 AC XY: 10721 AN XY: 74394

African (AFR) AF: 0.0313 AC: 1300 AN: 41534

American (AMR) AF: 0.213 AC: 3262 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 774 AN: 3470

East Asian (EAS) AF: 0.151 AC: 784 AN: 5182

South Asian (SAS) AF: 0.242 AC: 1168 AN: 4818

European-Finnish (FIN) AF: 0.201 AC: 2130 AN: 10586

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11103 AN: 67976

Other (OTH) AF: 0.143 AC: 301 AN: 2112

Alfa AF: 0.152 Hom.: 249

Bravo AF: 0.136

Asia WGS AF: 0.173 AC: 603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.9
DANN	Benign	0.57
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs2120902; hg19: chr10-70020222;