rs10490741

Variant names:

• chr2-137119394-G-A
• rs10490741
• NM_001316349.2:c.1369+4101G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-137119394-G-A
• chr2-137119394-G-C
• chr2-137119394-G-T

Variant summary

Our verdict is

Benign

<-10 Benign

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001316349.2(THSD7B):​c.1369+4101G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0508 in 152,230 control chromosomes in the GnomAD database, including 228 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 0.051 (228 hom., cov: 33)
• Consequence: THSD7B NM_001316349.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0844 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001316349.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	THSD7B	NM_001316349.2	MANE Select	c.1369+4101G>A		intron	N/A	NP_001303278.1	Q9C0I4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	THSD7B	ENST00000409968.6	TSL:5 MANE Select	c.1369+4101G>A		intron	N/A	ENSP00000387145.1	Q9C0I4

Frequencies

GnomAD3 genomes AF: 0.0507 AC: 7716 AN: 152112 Hom.: 228 Cov.: 33

Gnomad AFR AF: 0.0761

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0410

Gnomad ASJ AF: 0.0686

Gnomad EAS AF: 0.0910

Gnomad SAS AF: 0.0526

Gnomad FIN AF: 0.0742

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0308

Gnomad OTH AF: 0.0430

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

GnomAD4 genome AF: 0.0508 AC: 7726 AN: 152230 Hom.: 228 Cov.: 33 AF XY: 0.0521 AC XY: 3874 AN XY: 74424

African (AFR) AF: 0.0761 AC: 3162 AN: 41538

American (AMR) AF: 0.0409 AC: 625 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0686 AC: 238 AN: 3468

East Asian (EAS) AF: 0.0912 AC: 472 AN: 5174

South Asian (SAS) AF: 0.0518 AC: 250 AN: 4826

European-Finnish (FIN) AF: 0.0742 AC: 786 AN: 10594

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0308 AC: 2093 AN: 68022

Other (OTH) AF: 0.0449 AC: 95 AN: 2116

Alfa AF: 0.0450 Hom.: 131

Bravo AF: 0.0508

Asia WGS AF: 0.0720 AC: 250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.8
DANN	Benign	0.52
PhyloP100		-0.29
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10490741;

hg19: chr2-137876964;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline