5-149071352-C-G

Variant names:

• chr5-149071352-C-G
• rs2915806
• ENST00000515519.7:n.631C>G

Variant summary

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

The ENST00000515519.7(SH3TC2-DT):​n.631C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 152,050 control chromosomes in the GnomAD database, including 20,237 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 0.50 (20233 hom., cov: 32)
  • Exomes 𝑓: 0.42 (4 hom.)
• Consequence: SH3TC2-DT ENST00000515519.7 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.713
• Publications: 1 publications found

Genes affected

SH3TC2-DT (HGNC:52905): (SH3TC2 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SH3TC2-DT	NR_122044.1	n.467+6994C>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SH3TC2-DT	ENST00000515519.7	n.631C>G		non_coding_transcript_exon_variant	Exon 4 of 4	5
SH3TC2-DT	ENST00000787335.1	n.499C>G		non_coding_transcript_exon_variant	Exon 3 of 3
SH3TC2-DT	ENST00000787336.1	n.495C>G		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75589 AN: 151894 Hom.: 20186 Cov.: 32

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.483

GnomAD4 exome AF: 0.421 AC: 16 AN: 38 Hom.: 4 Cov.: 0 AF XY: 0.375 AC XY: 9 AN XY: 24

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.375 AC: 3 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.462 AC: 12 AN: 26

Other (OTH) AF: 0.250 AC: 1 AN: 4

GnomAD4 genome AF: 0.498 AC: 75690 AN: 152012 Hom.: 20233 Cov.: 32 AF XY: 0.502 AC XY: 37293 AN XY: 74300

African (AFR) AF: 0.684 AC: 28359 AN: 41450

American (AMR) AF: 0.507 AC: 7751 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1632 AN: 3468

East Asian (EAS) AF: 0.456 AC: 2357 AN: 5172

South Asian (SAS) AF: 0.649 AC: 3125 AN: 4818

European-Finnish (FIN) AF: 0.370 AC: 3897 AN: 10542

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27024 AN: 67954

Other (OTH) AF: 0.485 AC: 1025 AN: 2114

Alfa AF: 0.287 Hom.: 707

Bravo AF: 0.512

Asia WGS AF: 0.539 AC: 1876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.70
DANN	Benign	0.38
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs2915806; hg19: chr5-148450915;