4-8188492-T-G

Variant names:

• chr4-8188492-T-G
• rs1078701
• ENST00000874439.1:c.-29+6282T>G

Variant summary

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

The NM_001410712.1(SH3TC1):​c.-29+6282T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.966 in 152,322 control chromosomes in the GnomAD database, including 71,180 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 0.97 (71180 hom., cov: 35)
• Consequence: SH3TC1 NM_001410712.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.306
• Publications: 1 publications found

Genes affected

SH3TC1 (HGNC:26009): (SH3 domain and tetratricopeptide repeats 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.983 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001410712.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SH3TC1	NM_001410712.1		c.-29+6282T>G		intron	N/A	NP_001397641.1	A0A804HI81

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SH3TC1	ENST00000874439.1		c.-29+6282T>G		intron	N/A	ENSP00000544498.1
	SH3TC1	ENST00000508641.2	TSL:4	c.-57+6282T>G		intron	N/A	ENSP00000426035.2	H0YA34
	SH3TC1	ENST00000510763.5	TSL:4	n.139+6282T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.966 AC: 147020 AN: 152204 Hom.: 71134 Cov.: 35

Gnomad AFR AF: 0.909

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.979

Gnomad ASJ AF: 0.939

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.995

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.990

Gnomad OTH AF: 0.951

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

GnomAD4 genome AF: 0.966 AC: 147126 AN: 152322 Hom.: 71180 Cov.: 35 AF XY: 0.967 AC XY: 72005 AN XY: 74482

African (AFR) AF: 0.909 AC: 37760 AN: 41558

American (AMR) AF: 0.979 AC: 14981 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.939 AC: 3261 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5167 AN: 5168

South Asian (SAS) AF: 0.995 AC: 4804 AN: 4830

European-Finnish (FIN) AF: 0.999 AC: 10620 AN: 10630

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.990 AC: 67333 AN: 68040

Other (OTH) AF: 0.951 AC: 2009 AN: 2112

Alfa AF: 0.979 Hom.: 87111

Bravo AF: 0.962

Asia WGS AF: 0.991 AC: 3446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.7
DANN	Benign	0.43
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs1078701; hg19: chr4-8190219;