rs1438405

Positions:

• chr4-67992826-A-G

Variant summary

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

The NR_033737.2(TMPRSS11GP):​n.308-981T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 152,086 control chromosomes in the GnomAD database, including 32,655 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 0.62 (32655 hom., cov: 32)
• Consequence: TMPRSS11GP NR_033737.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.56

Genes affected

TMPRSS11GP (HGNC:42983): (transmembrane serine protease 11G, pseudogene)

UBA6-DT (HGNC:49083): (UBA6 divergent transcript)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMPRSS11GP	NR_033737.2	n.308-981T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMPRSS11GP	ENST00000431070.6	n.1043-981T>C		intron_variant, non_coding_transcript_variant
UBA6-DT	ENST00000500538.7	n.1988-69781A>G		intron_variant, non_coding_transcript_variant		1
	ENST00000502496.1	n.356-981T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93598 AN: 151968 Hom.: 32651 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.616 AC: 93627 AN: 152086 Hom.: 32655 Cov.: 32 AF XY: 0.617 AC XY: 45859 AN XY: 74350

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.565

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.832

Gnomad4 SAS AF: 0.725

Gnomad4 FIN AF: 0.745

Gnomad4 NFE AF: 0.785

Gnomad4 OTH AF: 0.614

Alfa AF: 0.739 Hom.: 19363

Bravo AF: 0.585

Asia WGS AF: 0.735 AC: 2557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.7
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1438405; hg19: chr4-68858544;