rs10484676

Variant names:

• chr6-147983562-T-C
• rs10484676
• ENST00000773311.1:n.49-35216T>C

Variant summary

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

The ENST00000773311.1(ENSG00000287976):​n.49-35216T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.088 in 152,288 control chromosomes in the GnomAD database, including 607 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 0.088 (607 hom., cov: 33)
• Consequence: ENSG00000287976 ENST00000773311.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11
• Publications: 0 publications found

Genes affected

ENSG00000287976 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000773311.1. 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
	ENSG00000287976	ENST00000773311.1		n.49-35216T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0880 AC: 13392 AN: 152170 Hom.: 608 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0570

Gnomad ASJ AF: 0.0381

Gnomad EAS AF: 0.0113

Gnomad SAS AF: 0.0128

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0931

Gnomad OTH AF: 0.0765

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

GnomAD4 genome AF: 0.0880 AC: 13405 AN: 152288 Hom.: 607 Cov.: 33 AF XY: 0.0861 AC XY: 6414 AN XY: 74468

African (AFR) AF: 0.110 AC: 4572 AN: 41558

American (AMR) AF: 0.0570 AC: 873 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0381 AC: 132 AN: 3468

East Asian (EAS) AF: 0.0112 AC: 58 AN: 5190

South Asian (SAS) AF: 0.0130 AC: 63 AN: 4832

European-Finnish (FIN) AF: 0.107 AC: 1130 AN: 10602

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0931 AC: 6329 AN: 68012

Other (OTH) AF: 0.0757 AC: 160 AN: 2114

Alfa AF: 0.0880 Hom.: 313

Bravo AF: 0.0865

Asia WGS AF: 0.0260 AC: 90 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.15
DANN	Benign	0.77
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs10484676; hg19: chr6-148304698;