4-8224847-G-C

Variant names:

• chr4-8224847-G-C
• rs2279195
• NM_018986.5:c.1244-328G>C

Variant summary

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

The NM_018986.5(SH3TC1):​c.1244-328G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 152,086 control chromosomes in the GnomAD database, including 11,727 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 0.39 (11727 hom., cov: 33)
• Consequence: SH3TC1 NM_018986.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SH3TC1	NM_018986.5	c.1244-328G>C		intron_variant	Intron 10 of 17	ENST00000245105.8	NP_061859.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SH3TC1	ENST00000245105.8	c.1244-328G>C		intron_variant	Intron 10 of 17	2	NM_018986.5	ENSP00000245105.3

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58652 AN: 151970 Hom.: 11719 Cov.: 33

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.386 AC: 58693 AN: 152086 Hom.: 11727 Cov.: 33 AF XY: 0.391 AC XY: 29093 AN XY: 74360

African (AFR) AF: 0.435 AC: 18051 AN: 41468

American (AMR) AF: 0.480 AC: 7341 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1200 AN: 3472

East Asian (EAS) AF: 0.537 AC: 2767 AN: 5156

South Asian (SAS) AF: 0.302 AC: 1458 AN: 4828

European-Finnish (FIN) AF: 0.407 AC: 4315 AN: 10596

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.330 AC: 22423 AN: 67974

Other (OTH) AF: 0.370 AC: 779 AN: 2108

Alfa AF: 0.215 Hom.: 458

Bravo AF: 0.394

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.58
PhyloP100		0.47
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: rs2279195; hg19: chr4-8226574;