chr2-137469872-G-A

Variant names:

• chr2-137469872-G-A
• rs1869324
• NM_001316349.2:c.3138+18849G>A

Variant summary

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

The NM_001316349.2(THSD7B):​c.3138+18849G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0774 in 152,192 control chromosomes in the GnomAD database, including 682 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 0.077 (682 hom., cov: 32)
• Consequence: THSD7B NM_001316349.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44
• Publications: 4 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=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
THSD7B	NM_001316349.2	c.3138+18849G>A		intron_variant	Intron 15 of 27	ENST00000409968.6	NP_001303278.1
THSD7B	XM_047445935.1	c.2715+18849G>A		intron_variant	Intron 15 of 27		XP_047301891.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
THSD7B	ENST00000409968.6	c.3138+18849G>A		intron_variant	Intron 15 of 27	5	NM_001316349.2	ENSP00000387145.1

Frequencies

GnomAD3 genomes AF: 0.0775 AC: 11782 AN: 152074 Hom.: 682 Cov.: 32

Gnomad AFR AF: 0.0216

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.0452

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0393

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.0641

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

GnomAD4 genome AF: 0.0774 AC: 11776 AN: 152192 Hom.: 682 Cov.: 32 AF XY: 0.0768 AC XY: 5718 AN XY: 74412

African (AFR) AF: 0.0215 AC: 893 AN: 41544

American (AMR) AF: 0.0452 AC: 690 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0323 AC: 112 AN: 3468

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5180

South Asian (SAS) AF: 0.0385 AC: 186 AN: 4828

European-Finnish (FIN) AF: 0.143 AC: 1517 AN: 10594

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8159 AN: 67988

Other (OTH) AF: 0.0644 AC: 136 AN: 2112

Alfa AF: 0.0917 Hom.: 863

Bravo AF: 0.0660

Asia WGS AF: 0.0320 AC: 113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	14
DANN	Benign	0.54
PhyloP100		1.4
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: rs1869324; hg19: chr2-138227442;