chr3-46609503-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

Genes affected

ENSG00000283877 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505797.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283877	ENST00000505797.1	TSL:3	n.*195-7680C>T		intron	N/A	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

African (AFR) AF: 0.0228 AC: 949 AN: 41562

American (AMR) AF: 0.0686 AC: 1050 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0412 AC: 143 AN: 3470

East Asian (EAS) AF: 0.148 AC: 763 AN: 5168

South Asian (SAS) AF: 0.112 AC: 538 AN: 4820

European-Finnish (FIN) AF: 0.0464 AC: 492 AN: 10612

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0496 AC: 3376 AN: 68026

Other (OTH) AF: 0.0620 AC: 131 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	2.2
DANN	Benign	0.75
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs2176862; hg19: chr3-46650993;