7-42602670-T-C

Variant names:

• chr7-42602670-T-C
• rs949459
• ENST00000752533.1:n.478-4321A>G

Variant summary

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

The ENST00000752533.1(ENSG00000298023):​n.478-4321A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.796 in 152,118 control chromosomes in the GnomAD database, including 48,531 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 0.80 (48531 hom., cov: 31)
• Consequence: ENSG00000298023 ENST00000752533.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.473
• Publications: 2 publications found

Genes affected

ENSG00000298023 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.936 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
ENSG00000298023	ENST00000752533.1	n.478-4321A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.795 AC: 120906 AN: 152000 Hom.: 48468 Cov.: 31

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.958

Gnomad SAS AF: 0.936

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.761

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.796 AC: 121028 AN: 152118 Hom.: 48531 Cov.: 31 AF XY: 0.803 AC XY: 59708 AN XY: 74364

African (AFR) AF: 0.862 AC: 35766 AN: 41510

American (AMR) AF: 0.805 AC: 12312 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.720 AC: 2495 AN: 3466

East Asian (EAS) AF: 0.958 AC: 4957 AN: 5174

South Asian (SAS) AF: 0.936 AC: 4517 AN: 4824

European-Finnish (FIN) AF: 0.781 AC: 8247 AN: 10564

Middle Eastern (MID) AF: 0.753 AC: 220 AN: 292

European-Non Finnish (NFE) AF: 0.739 AC: 50214 AN: 67974

Other (OTH) AF: 0.784 AC: 1651 AN: 2106

Alfa AF: 0.778 Hom.: 7413

Bravo AF: 0.796

Asia WGS AF: 0.932 AC: 3236 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.63
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs949459; hg19: chr7-42642269;