6-82401922-C-T

Variant names:

• chr6-82401922-C-T
• rs4706947
• ENST00000773976.1:n.203-16605G>A

Variant summary

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

The ENST00000773976.1(ENSG00000300778):​n.203-16605G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 152,026 control chromosomes in the GnomAD database, including 10,319 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 0.36 (10319 hom., cov: 32)
• Consequence: ENSG00000300778 ENST00000773976.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100
• Publications: 2 publications found

Genes affected

ENSG00000300778 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000773976.1. 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
	ENSG00000300778	ENST00000773976.1		n.203-16605G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55299 AN: 151908 Hom.: 10307 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.364 AC: 55341 AN: 152026 Hom.: 10319 Cov.: 32 AF XY: 0.361 AC XY: 26829 AN XY: 74296

African (AFR) AF: 0.371 AC: 15386 AN: 41462

American (AMR) AF: 0.352 AC: 5373 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1375 AN: 3472

East Asian (EAS) AF: 0.606 AC: 3126 AN: 5162

South Asian (SAS) AF: 0.468 AC: 2251 AN: 4814

European-Finnish (FIN) AF: 0.292 AC: 3087 AN: 10560

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23666 AN: 67974

Other (OTH) AF: 0.322 AC: 679 AN: 2108

Alfa AF: 0.364 Hom.: 1293

Bravo AF: 0.364

Asia WGS AF: 0.528 AC: 1837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.4
DANN	Benign	0.30
PhyloP100		0.0010

Splicing

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

Other links and lift over

dbSNP: rs4706947; hg19: chr6-83111639;