rs2600178

Positions:

• chr3-9360377-C-A
• chr3-9360377-C-G
• chr3-9360377-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000468186.5(THUMPD3-AS1):​n.2876-10311G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 152,152 control chromosomes in the GnomAD database, including 39,746 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 0.72 (39746 hom., cov: 33)
• Consequence: THUMPD3-AS1 ENST00000468186.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546

Genes affected

THUMPD3-AS1 (HGNC:44478): (THUMPD3 antisense RNA 1)

(HGNC:):

SRGAP3 (HGNC:19744): (SLIT-ROBO Rho GTPase activating protein 3) Predicted to enable GTPase activator activity. Predicted to be involved in negative regulation of cell migration. Predicted to be located in cytosol. Predicted to be active in cytoplasm. [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 (EAS) allele frequency at 95% confidence interval = 0.962 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SRGAP3	XM_024453843.2	c.-522+2463G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
THUMPD3-AS1	ENST00000468186.5	n.2876-10311G>T		intron_variant, non_coding_transcript_variant		1
	ENST00000491930.2	n.190+2463G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109163 AN: 152034 Hom.: 39716 Cov.: 33

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.742

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.729

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

GnomAD4 genome AF: 0.718 AC: 109247 AN: 152152 Hom.: 39746 Cov.: 33 AF XY: 0.728 AC XY: 54184 AN XY: 74382

Gnomad4 AFR AF: 0.640

Gnomad4 AMR AF: 0.785

Gnomad4 ASJ AF: 0.742

Gnomad4 EAS AF: 0.985

Gnomad4 SAS AF: 0.888

Gnomad4 FIN AF: 0.737

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.732

Alfa AF: 0.717 Hom.: 15520

Bravo AF: 0.718

Asia WGS AF: 0.887 AC: 3085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.59

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2600178; hg19: chr3-9402061;