rs6552135

Variant names:

• chr4-67963811-A-G
• rs6552135
• ENST00000500538.7:n.1988-98796A>G

Your query was ambiguous. Multiple possible variants found:

• chr4-67963811-A-G
• chr4-67963811-A-T

Variant summary

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

The ENST00000334830.11(TMPRSS11A):​c.-418T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 153,446 control chromosomes in the GnomAD database, including 15,672 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 0.40 (15456 hom., cov: 32)
  • Exomes 𝑓: 0.55 (216 hom.)
• Consequence: TMPRSS11A ENST00000334830.11 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.18

Genes affected

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

TMPRSS11A (HGNC:27954): (transmembrane serine protease 11A) Predicted to enable serine-type endopeptidase activity. Predicted to be involved in proteolysis. Predicted to be located in extracellular region. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBA6-DT	ENST00000500538.7	n.1988-98796A>G		intron_variant	Intron 6 of 7	1
TMPRSS11A	ENST00000334830.11	c.-418T>C		5_prime_UTR_variant	Exon 1 of 10	2		ENSP00000334611.7
UBA6-DT	ENST00000663060.1	n.1209-54697A>G		intron_variant	Intron 4 of 6
UBA6-DT	ENST00000667140.1	n.1469-54697A>G		intron_variant	Intron 6 of 9

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61244 AN: 151956 Hom.: 15462 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.394

GnomAD4 exome AF: 0.547 AC: 750 AN: 1370 Hom.: 216 Cov.: 0 AF XY: 0.569 AC XY: 387 AN XY: 680

Gnomad4 AFR exome AF: 0.0714

Gnomad4 AMR exome AF: 0.333

Gnomad4 ASJ exome AF: 0.395

Gnomad4 EAS exome AF: 0.538

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.413

Gnomad4 NFE exome AF: 0.612

Gnomad4 OTH exome AF: 0.447

GnomAD4 genome AF: 0.403 AC: 61240 AN: 152076 Hom.: 15456 Cov.: 32 AF XY: 0.398 AC XY: 29590 AN XY: 74320

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.505

Gnomad4 NFE AF: 0.570

Gnomad4 OTH AF: 0.392

Alfa AF: 0.493 Hom.: 2864

Bravo AF: 0.377

Asia WGS AF: 0.392 AC: 1352 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	10
DANN	Benign	0.77

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: rs6552135; hg19: chr4-68829529;