ENST00000748463.1:n.65-7048T>C

Variant names:

• chr6-27210249-T-C
• rs858985
• ENST00000748463.1:n.65-7048T>C

Variant summary

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

The ENST00000748463.1(ENSG00000297504):​n.65-7048T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.894 in 152,200 control chromosomes in the GnomAD database, including 61,094 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 0.89 (61094 hom., cov: 32)
• Consequence: ENSG00000297504 ENST00000748463.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.589
• Publications: 3 publications found

Genes affected

ENSG00000297504 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000748463.1. 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
	ENSG00000297504	ENST00000748463.1		n.65-7048T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.895 AC: 136039 AN: 152082 Hom.: 61059 Cov.: 32

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.912

Gnomad AMR AF: 0.940

Gnomad ASJ AF: 0.980

Gnomad EAS AF: 0.948

Gnomad SAS AF: 0.976

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.906

Gnomad OTH AF: 0.922

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

GnomAD4 genome AF: 0.894 AC: 136130 AN: 152200 Hom.: 61094 Cov.: 32 AF XY: 0.892 AC XY: 66333 AN XY: 74398

African (AFR) AF: 0.863 AC: 35833 AN: 41504

American (AMR) AF: 0.940 AC: 14374 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.980 AC: 3402 AN: 3472

East Asian (EAS) AF: 0.948 AC: 4899 AN: 5170

South Asian (SAS) AF: 0.977 AC: 4720 AN: 4830

European-Finnish (FIN) AF: 0.777 AC: 8225 AN: 10592

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.906 AC: 61614 AN: 68018

Other (OTH) AF: 0.922 AC: 1948 AN: 2112

Alfa AF: 0.909 Hom.: 238241

Bravo AF: 0.903

Asia WGS AF: 0.964 AC: 3355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.62
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs858985; hg19: chr6-27178028;