chr14-64368800-A-G

Variant names:

• chr14-64368800-A-G
• rs2987981
• ENST00000447107.1:n.264+5603T>C

Variant summary

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

The ENST00000556556.2(ENSG00000293482):​n.358+5596T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 152,044 control chromosomes in the GnomAD database, including 6,240 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 0.27 (6240 hom., cov: 32)
• Consequence: ENSG00000293482 ENST00000556556.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470
• Publications: 9 publications found

Genes affected

TEX21P (HGNC:35455): (testis expressed 21, pseudogene)

ENSG00000293482 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000556556.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX21P	ENST00000447107.1	TSL:6	n.264+5603T>C		intron	N/A
	ENSG00000293482	ENST00000556556.2	TSL:4	n.358+5596T>C		intron	N/A
	ENSG00000293482	ENST00000641343.1		n.347+5596T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.270 AC: 40981 AN: 151926 Hom.: 6239 Cov.: 32

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.270 AC: 41002 AN: 152044 Hom.: 6240 Cov.: 32 AF XY: 0.264 AC XY: 19587 AN XY: 74306

African (AFR) AF: 0.400 AC: 16593 AN: 41432

American (AMR) AF: 0.200 AC: 3061 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1051 AN: 3470

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5182

South Asian (SAS) AF: 0.212 AC: 1020 AN: 4818

European-Finnish (FIN) AF: 0.181 AC: 1912 AN: 10572

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16449 AN: 67994

Other (OTH) AF: 0.263 AC: 554 AN: 2104

Alfa AF: 0.254 Hom.: 8762

Bravo AF: 0.274

Asia WGS AF: 0.126 AC: 438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.4
DANN	Benign	0.73
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs2987981; hg19: chr14-64835518;