rs2370192

Variant names:

• chr2-136869414-T-A
• rs2370192
• NM_001316349.2:c.-35-12730T>A

Your query was ambiguous. Multiple possible variants found:

• chr2-136869414-T-A
• chr2-136869414-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001316349.2(THSD7B):​c.-35-12730T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0138 in 152,342 control chromosomes in the GnomAD database, including 30 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 0.014 (30 hom., cov: 33)
• Consequence: THSD7B NM_001316349.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53

Genes affected

THSD7B (HGNC:29348): (thrombospondin type 1 domain containing 7B) Predicted to be involved in actin cytoskeleton reorganization. Predicted to be integral component of membrane. Predicted to be active in 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=-0.64).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0138 (2098/152342) while in subpopulation NFE AF= 0.0212 (1445/68024). AF 95% confidence interval is 0.0203. There are 30 homozygotes in gnomad4. There are 932 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 30 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
THSD7B	NM_001316349.2	c.-35-12730T>A		intron_variant	Intron 1 of 27	ENST00000409968.6	NP_001303278.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
THSD7B	ENST00000409968.6	c.-35-12730T>A		intron_variant	Intron 1 of 27	5	NM_001316349.2	ENSP00000387145.1
THSD7B	ENST00000472720.5	n.-35-12730T>A		intron_variant	Intron 1 of 3	5		ENSP00000473349.1

Frequencies

GnomAD3 genomes AF: 0.0138 AC: 2100 AN: 152224 Hom.: 30 Cov.: 33

Gnomad AFR AF: 0.00371

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0113

Gnomad ASJ AF: 0.0562

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00517

Gnomad FIN AF: 0.00658

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0212

Gnomad OTH AF: 0.0148

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

GnomAD4 genome AF: 0.0138 AC: 2098 AN: 152342 Hom.: 30 Cov.: 33 AF XY: 0.0125 AC XY: 932 AN XY: 74500

Gnomad4 AFR AF: 0.00370

Gnomad4 AMR AF: 0.0113

Gnomad4 ASJ AF: 0.0562

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.00518

Gnomad4 FIN AF: 0.00658

Gnomad4 NFE AF: 0.0212

Gnomad4 OTH AF: 0.0142

Alfa AF: 0.00240 Hom.: 0

Bravo AF: 0.0141

Asia WGS AF: 0.00869 AC: 30 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	14
DANN	Benign	0.91

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: rs2370192; hg19: chr2-137626984;