rs3741869

Positions:

• chr12-30995252-G-A
• chr12-30995252-G-C

Variant summary

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

The NM_001370302.1(TSPAN11):​c.*3337G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,370 control chromosomes in the GnomAD database, including 1,554 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 0.13 (1554 hom., cov: 33)
  • Exomes 𝑓: 0.092 (0 hom.)
• Consequence: TSPAN11 NM_001370302.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890

Genes affected

TSPAN11 (HGNC:30795): (tetraspanin 11) Predicted to be involved in cell migration. Predicted to be integral component of membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

TSPAN11-AS1 (HGNC:56687): (TSPAN11 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSPAN11	NM_001370302.1	c.*3337G>A		3_prime_UTR_variant	8/8	ENST00000546076.6	NP_001357231.1
TSPAN11-AS1	XR_007063261.1	n.294+3935C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TSPAN11	ENST00000546076.6	c.*3337G>A		3_prime_UTR_variant	8/8	2	NM_001370302.1	ENSP00000437403	P1
TSPAN11	ENST00000261177.10	c.*3337G>A		3_prime_UTR_variant	8/8	1		ENSP00000261177	P1
TSPAN11-AS1	ENST00000613860.4	n.401+735C>T		intron_variant, non_coding_transcript_variant		5
TSPAN11-AS1	ENST00000625497.2	n.228+3935C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20052 AN: 152130 Hom.: 1560 Cov.: 33

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.0953

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.0911

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.148

GnomAD4 exome AF: 0.0917 AC: 11 AN: 120 Hom.: 0 Cov.: 0 AF XY: 0.0978 AC XY: 9 AN XY: 92

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0918

Gnomad4 OTH exome AF: 0.100

GnomAD4 genome AF: 0.132 AC: 20035 AN: 152250 Hom.: 1554 Cov.: 33 AF XY: 0.132 AC XY: 9804 AN XY: 74426

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.0952

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.351

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.0911

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.147

Alfa AF: 0.134 Hom.: 1931

Bravo AF: 0.131

Asia WGS AF: 0.301 AC: 1043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.85
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3741869; hg19: chr12-31148187;