rs979976

Variant names:

• chr2-137011132-A-C
• rs979976
• NM_001316349.2:c.140-45288A>C

Your query was ambiguous. Multiple possible variants found:

• chr2-137011132-A-C
• chr2-137011132-A-T

Variant summary

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

The NM_001316349.2(THSD7B):​c.140-45288A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 151,940 control chromosomes in the GnomAD database, including 29,159 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 0.60 (29159 hom., cov: 31)
• Consequence: THSD7B NM_001316349.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.820
• Publications: 8 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
THSD7B	NM_001316349.2	c.140-45288A>C		intron_variant	Intron 2 of 27	ENST00000409968.6	NP_001303278.1
THSD7B	XM_047445935.1	c.-284-45288A>C		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.140-45288A>C		intron_variant	Intron 2 of 27	5	NM_001316349.2	ENSP00000387145.1
THSD7B	ENST00000472720.5	n.*106-45288A>C		intron_variant	Intron 3 of 3	5		ENSP00000473349.1

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91623 AN: 151822 Hom.: 29153 Cov.: 31

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.603 AC: 91652 AN: 151940 Hom.: 29159 Cov.: 31 AF XY: 0.612 AC XY: 45443 AN XY: 74272

African (AFR) AF: 0.385 AC: 15947 AN: 41420

American (AMR) AF: 0.655 AC: 10001 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2544 AN: 3470

East Asian (EAS) AF: 0.644 AC: 3307 AN: 5136

South Asian (SAS) AF: 0.760 AC: 3665 AN: 4820

European-Finnish (FIN) AF: 0.768 AC: 8109 AN: 10556

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.675 AC: 45846 AN: 67962

Other (OTH) AF: 0.623 AC: 1313 AN: 2108

Alfa AF: 0.650 Hom.: 143711

Bravo AF: 0.581

Asia WGS AF: 0.681 AC: 2366 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.17
DANN	Benign	0.77
PhyloP100		-0.82
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: rs979976; hg19: chr2-137768702;