2-137012082-A-G

Variant names:

• chr2-137012082-A-G
• rs1432241
• NM_001316349.2:c.140-44338A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001316349.2(THSD7B):​c.140-44338A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.898 in 152,190 control chromosomes in the GnomAD database, including 61,838 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 0.90 (61838 hom., cov: 32)
• Consequence: THSD7B NM_001316349.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
THSD7B	NM_001316349.2	c.140-44338A>G		intron_variant	Intron 2 of 27	ENST00000409968.6	NP_001303278.1
THSD7B	XM_047445935.1	c.-284-44338A>G		intron_variant	Intron 2 of 27		XP_047301891.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
THSD7B	ENST00000409968.6	c.140-44338A>G		intron_variant	Intron 2 of 27	5	NM_001316349.2	ENSP00000387145.1
THSD7B	ENST00000472720.5	n.*106-44338A>G		intron_variant	Intron 3 of 3	5		ENSP00000473349.1

Frequencies

GnomAD3 genomes AF: 0.898 AC: 136596 AN: 152072 Hom.: 61795 Cov.: 32

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.962

Gnomad AMR AF: 0.905

Gnomad ASJ AF: 0.979

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.981

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.935

Gnomad OTH AF: 0.915

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

GnomAD4 genome AF: 0.898 AC: 136696 AN: 152190 Hom.: 61838 Cov.: 32 AF XY: 0.902 AC XY: 67111 AN XY: 74410

African (AFR) AF: 0.782 AC: 32473 AN: 41500

American (AMR) AF: 0.904 AC: 13822 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.979 AC: 3398 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5161 AN: 5166

South Asian (SAS) AF: 0.981 AC: 4736 AN: 4828

European-Finnish (FIN) AF: 0.983 AC: 10435 AN: 10614

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.935 AC: 63582 AN: 68012

Other (OTH) AF: 0.916 AC: 1933 AN: 2110

Alfa AF: 0.918 Hom.: 13390

Bravo AF: 0.884

Asia WGS AF: 0.981 AC: 3407 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.3
DANN	Benign	0.56
PhyloP100		0.21
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

Other links and lift over

dbSNP: rs1432241; hg19: chr2-137769652;