NM_001316349.2:c.1370-16764T>C

Variant names:

• chr2-137143449-T-C
• rs16838223
• NM_001316349.2:c.1370-16764T>C

Variant summary

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

The NM_001316349.2(THSD7B):​c.1370-16764T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 151,966 control chromosomes in the GnomAD database, including 10,612 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 0.36 (10612 hom., cov: 33)
• Consequence: THSD7B NM_001316349.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.517 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	THSD7B	NM_001316349.2	MANE Select	c.1370-16764T>C		intron	N/A	NP_001303278.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	THSD7B	ENST00000409968.6	TSL:5 MANE Select	c.1370-16764T>C		intron	N/A	ENSP00000387145.1

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55254 AN: 151848 Hom.: 10596 Cov.: 33

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.364 AC: 55307 AN: 151966 Hom.: 10612 Cov.: 33 AF XY: 0.362 AC XY: 26855 AN XY: 74272

African (AFR) AF: 0.469 AC: 19443 AN: 41456

American (AMR) AF: 0.384 AC: 5860 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1220 AN: 3472

East Asian (EAS) AF: 0.534 AC: 2758 AN: 5164

South Asian (SAS) AF: 0.343 AC: 1650 AN: 4808

European-Finnish (FIN) AF: 0.252 AC: 2674 AN: 10594

Middle Eastern (MID) AF: 0.445 AC: 130 AN: 292

European-Non Finnish (NFE) AF: 0.301 AC: 20473 AN: 67904

Other (OTH) AF: 0.395 AC: 836 AN: 2114

Alfa AF: 0.317 Hom.: 13242

Bravo AF: 0.381

Asia WGS AF: 0.426 AC: 1483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.5
DANN	Benign	0.70
PhyloP100		0.24
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: rs16838223; hg19: chr2-137901019;