rs979976

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
THSD7B	NM_001316349.2	c.140-45288A>C		intron_variant		ENST00000409968.6	NP_001303278.1
THSD7B	XM_047445935.1	c.-284-45288A>C		intron_variant			XP_047301891.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
THSD7B	ENST00000409968.6	c.140-45288A>C		intron_variant		5	NM_001316349.2	ENSP00000387145	P1
THSD7B	ENST00000472720.5	c.*106-45288A>C		intron_variant, NMD_transcript_variant		5		ENSP00000473349

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

Gnomad4 AFR AF: 0.385

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.733

Gnomad4 EAS AF: 0.644

Gnomad4 SAS AF: 0.760

Gnomad4 FIN AF: 0.768

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.623

Alfa AF: 0.666 Hom.: 67041

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs979976; hg19: chr2-137768702;