rs3741869

Variant names:

• chr12-30995252-G-A
• rs3741869
• NM_001370302.1:c.*3337G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TSPAN11	NM_001370302.1	c.*3337G>A		3_prime_UTR_variant	Exon 8 of 8	ENST00000546076.6	NP_001357231.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSPAN11	ENST00000546076.6	c.*3337G>A		3_prime_UTR_variant	Exon 8 of 8	2	NM_001370302.1	ENSP00000437403.1
TSPAN11	ENST00000261177.10	c.*3337G>A		3_prime_UTR_variant	Exon 8 of 8	1		ENSP00000261177.9
TSPAN11-AS1	ENST00000613860.4	n.401+735C>T		intron_variant	Intron 4 of 5	5
TSPAN11-AS1	ENST00000625497.2	n.228+3935C>T		intron_variant	Intron 2 of 3	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

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.0918 AC: 9 AN: 98

Other (OTH) AF: 0.100 AC: 1 AN: 10

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

African (AFR) AF: 0.111 AC: 4611 AN: 41558

American (AMR) AF: 0.0952 AC: 1456 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 428 AN: 3468

East Asian (EAS) AF: 0.351 AC: 1810 AN: 5164

South Asian (SAS) AF: 0.263 AC: 1264 AN: 4814

European-Finnish (FIN) AF: 0.0911 AC: 968 AN: 10620

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.131 AC: 8897 AN: 68004

Other (OTH) AF: 0.147 AC: 310 AN: 2114

Alfa AF: 0.134 Hom.: 2752

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
PhyloP100		-0.089
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs3741869; hg19: chr12-31148187;