ENST00000748006.1:n.365-514T>G

Variant names:

• chr6-116568413-T-G
• rs980214
• ENST00000748006.1:n.365-514T>G

Variant summary

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

The ENST00000748006.1(ENSG00000297462):​n.365-514T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.685 in 152,068 control chromosomes in the GnomAD database, including 35,966 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 0.68 (35966 hom., cov: 32)
• Consequence: ENSG00000297462 ENST00000748006.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.435
• Publications: 3 publications found

Genes affected

ENSG00000297462 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297462	ENST00000748006.1	n.365-514T>G		intron_variant	Intron 1 of 1
ENSG00000297462	ENST00000748007.1	n.328-514T>G		intron_variant	Intron 2 of 2
ENSG00000297462	ENST00000748008.1	n.80-514T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.685 AC: 104055 AN: 151948 Hom.: 35925 Cov.: 32

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.685 AC: 104153 AN: 152068 Hom.: 35966 Cov.: 32 AF XY: 0.689 AC XY: 51218 AN XY: 74324

African (AFR) AF: 0.705 AC: 29218 AN: 41456

American (AMR) AF: 0.731 AC: 11183 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.765 AC: 2653 AN: 3470

East Asian (EAS) AF: 0.892 AC: 4618 AN: 5178

South Asian (SAS) AF: 0.668 AC: 3230 AN: 4834

European-Finnish (FIN) AF: 0.687 AC: 7251 AN: 10552

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.641 AC: 43590 AN: 67966

Other (OTH) AF: 0.706 AC: 1492 AN: 2112

Alfa AF: 0.639 Hom.: 6225

Bravo AF: 0.694

Asia WGS AF: 0.772 AC: 2680 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	0.77
DANN	Benign	0.51
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs980214; hg19: chr6-116889576; COSMIC: COSV63972935;