6-4108520-T-C

Variant names:

• chr6-4108520-T-C
• rs1815510
• ENST00000360378.6:n.488-6934T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000427996.5(TEX56P):​n.663+9322T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 152,170 control chromosomes in the GnomAD database, including 4,682 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 0.24 (4682 hom., cov: 32)
• Consequence: TEX56P ENST00000427996.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211

Genes affected

TEX56P (HGNC:21620): (testis expressed 56, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEX56P	NR_104463.3	n.1050-6887T>C		intron_variant	Intron 3 of 7
TEX56P	NR_104464.3	n.671+9322T>C		intron_variant	Intron 2 of 5
TEX56P	NR_172627.1	n.1049+9322T>C		intron_variant	Intron 3 of 5
TEX56P	NR_172628.1	n.671+9322T>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEX56P	ENST00000360378.6	n.488-6934T>C		intron_variant	Intron 2 of 2	4
TEX56P	ENST00000427996.5	n.663+9322T>C		intron_variant	Intron 2 of 5	2
TEX56P	ENST00000436110.1	n.488-6887T>C		intron_variant	Intron 2 of 6	2

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36716 AN: 152054 Hom.: 4681 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.0202

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.241 AC: 36737 AN: 152170 Hom.: 4682 Cov.: 32 AF XY: 0.233 AC XY: 17363 AN XY: 74382

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.0202

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.255

Alfa AF: 0.247 Hom.: 2235

Bravo AF: 0.244

Asia WGS AF: 0.100 AC: 351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	14
DANN	Benign	0.96

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1815510; hg19: chr6-4108754;