6-47397221-T-C

Variant names:

• chr6-47397221-T-C
• rs4715005
• ENST00000663906.1:n.178A>G

Variant summary

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

The ENST00000663906.1(ENSG00000287485):​n.178A>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 0.722 in 152,128 control chromosomes in the GnomAD database, including 40,729 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 0.72 (40729 hom., cov: 33)
• Consequence: ENSG00000287485 ENST00000663906.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.48
• Publications: 5 publications found

Genes affected

ENSG00000287485 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375082	XR_926865.4	n.178A>G		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287485	ENST00000663906.1	n.178A>G		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000287485	ENST00000741072.1	n.822-44A>G		intron_variant	Intron 1 of 3
ENSG00000287485	ENST00000741073.1	n.272-44A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109736 AN: 152010 Hom.: 40702 Cov.: 33

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.928

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.722 AC: 109805 AN: 152128 Hom.: 40729 Cov.: 33 AF XY: 0.726 AC XY: 54026 AN XY: 74366

African (AFR) AF: 0.537 AC: 22272 AN: 41468

American (AMR) AF: 0.776 AC: 11855 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2543 AN: 3472

East Asian (EAS) AF: 0.928 AC: 4805 AN: 5180

South Asian (SAS) AF: 0.749 AC: 3615 AN: 4824

European-Finnish (FIN) AF: 0.849 AC: 8999 AN: 10594

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.786 AC: 53410 AN: 67988

Other (OTH) AF: 0.725 AC: 1529 AN: 2110

Alfa AF: 0.746 Hom.: 80290

Bravo AF: 0.708

Asia WGS AF: 0.824 AC: 2867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.050
DANN	Benign	0.33
PhyloP100		-4.5

Splicing

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

Other links and lift over

dbSNP: rs4715005; hg19: chr6-47364957;