3-46609503-C-T

Variant names:

• chr3-46609503-C-T
• rs2176862
• ENST00000505797.1:n.*195-7680C>T

Variant summary

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

The ENST00000505797.1(ENSG00000283877):​n.*195-7680C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0496 in 152,274 control chromosomes in the GnomAD database, including 242 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 0.050 (242 hom., cov: 32)
• Consequence: ENSG00000283877 ENST00000505797.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117

Genes affected

ENSG00000283877 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283877	ENST00000505797.1	n.*195-7680C>T		intron_variant	Intron 3 of 3	3		ENSP00000490854.1

Frequencies

GnomAD3 genomes AF: 0.0497 AC: 7555 AN: 152156 Hom.: 242 Cov.: 32

Gnomad AFR AF: 0.0227

Gnomad AMI AF: 0.0901

Gnomad AMR AF: 0.0688

Gnomad ASJ AF: 0.0412

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0464

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0496

Gnomad OTH AF: 0.0632

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

GnomAD4 genome AF: 0.0496 AC: 7559 AN: 152274 Hom.: 242 Cov.: 32 AF XY: 0.0516 AC XY: 3841 AN XY: 74442

Gnomad4 AFR AF: 0.0228

Gnomad4 AMR AF: 0.0686

Gnomad4 ASJ AF: 0.0412

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.0464

Gnomad4 NFE AF: 0.0496

Gnomad4 OTH AF: 0.0620

Alfa AF: 0.0345 Hom.: 33

Bravo AF: 0.0502

Asia WGS AF: 0.120 AC: 416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	2.2
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2176862; hg19: chr3-46650993;