rs2120902

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KRT19P4		n.68260465T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KRT19P4	ENST00000443208.1	n.-92T>C		upstream_gene_variant		6

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 v4.3

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;