7-48920029-T-C

Variant names:

• chr7-48920029-T-C
• rs6583479
• ENST00000759941.1:n.399-2970A>G

Variant summary

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

The ENST00000759941.1(ENSG00000299032):​n.399-2970A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.779 in 151,238 control chromosomes in the GnomAD database, including 45,913 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 0.78 (45913 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000299032 ENST00000759941.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 0 publications found

Genes affected

ENSG00000299032 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 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
ENSG00000299032	ENST00000759941.1	n.399-2970A>G		intron_variant	Intron 1 of 2
ENSG00000299032	ENST00000759942.1	n.361+7788A>G		intron_variant	Intron 1 of 1
ENSG00000299032	ENST00000759943.1	n.279-2958A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.779 AC: 117709 AN: 151122 Hom.: 45862 Cov.: 31

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.771

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.828

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.779 AC: 117817 AN: 151238 Hom.: 45913 Cov.: 31 AF XY: 0.780 AC XY: 57670 AN XY: 73896

African (AFR) AF: 0.825 AC: 33907 AN: 41110

American (AMR) AF: 0.721 AC: 10968 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.771 AC: 2663 AN: 3456

East Asian (EAS) AF: 0.774 AC: 3995 AN: 5160

South Asian (SAS) AF: 0.753 AC: 3588 AN: 4762

European-Finnish (FIN) AF: 0.789 AC: 8305 AN: 10528

Middle Eastern (MID) AF: 0.829 AC: 242 AN: 292

European-Non Finnish (NFE) AF: 0.765 AC: 51804 AN: 67722

Other (OTH) AF: 0.766 AC: 1605 AN: 2094

Alfa AF: 0.689 Hom.: 1386

Bravo AF: 0.776

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.47
DANN	Benign	0.53
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs6583479; hg19: chr7-48959625;