NM_001316349.2:c.2500+46358G>A

Variant names:

• chr2-137322384-G-A
• rs10496768
• NM_001316349.2:c.2500+46358G>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.2500+46358G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0946 in 152,222 control chromosomes in the GnomAD database, including 889 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 0.095 (889 hom., cov: 32)
• Consequence: THSD7B NM_001316349.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170
• Publications: 3 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.132 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.2500+46358G>A		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.2500+46358G>A		intron	N/A	ENSP00000387145.1

Frequencies

GnomAD3 genomes AF: 0.0947 AC: 14410 AN: 152102 Hom.: 888 Cov.: 32

Gnomad AFR AF: 0.0239

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.0981

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0524

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.0946 AC: 14406 AN: 152222 Hom.: 889 Cov.: 32 AF XY: 0.0941 AC XY: 7003 AN XY: 74432

African (AFR) AF: 0.0239 AC: 991 AN: 41548

American (AMR) AF: 0.0980 AC: 1497 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 510 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5182

South Asian (SAS) AF: 0.0531 AC: 256 AN: 4824

European-Finnish (FIN) AF: 0.148 AC: 1563 AN: 10596

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9149 AN: 68006

Other (OTH) AF: 0.111 AC: 235 AN: 2108

Alfa AF: 0.116 Hom.: 829

Bravo AF: 0.0895

Asia WGS AF: 0.0250 AC: 86 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.52
PhyloP100		-0.17
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: rs10496768; hg19: chr2-138079954;