7-10279141-T-C

Variant names:

• chr7-10279141-T-C
• rs10224072
• ENST00000821578.1:n.116-307A>G

Variant summary

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

The ENST00000821578.1(ENSG00000306855):​n.116-307A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.792 in 151,888 control chromosomes in the GnomAD database, including 47,943 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 0.79 (47943 hom., cov: 31)
• Consequence: ENSG00000306855 ENST00000821578.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841
• Publications: 2 publications found

Genes affected

ENSG00000306855 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.883 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
ENSG00000306855	ENST00000821578.1	n.116-307A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.791 AC: 120126 AN: 151770 Hom.: 47891 Cov.: 31

Gnomad AFR AF: 0.891

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.792 AC: 120238 AN: 151888 Hom.: 47943 Cov.: 31 AF XY: 0.786 AC XY: 58370 AN XY: 74216

African (AFR) AF: 0.891 AC: 36939 AN: 41472

American (AMR) AF: 0.784 AC: 11921 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.804 AC: 2789 AN: 3468

East Asian (EAS) AF: 0.631 AC: 3240 AN: 5132

South Asian (SAS) AF: 0.713 AC: 3433 AN: 4812

European-Finnish (FIN) AF: 0.760 AC: 8044 AN: 10584

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.755 AC: 51238 AN: 67904

Other (OTH) AF: 0.782 AC: 1650 AN: 2110

Alfa AF: 0.761 Hom.: 70553

Bravo AF: 0.798

Asia WGS AF: 0.701 AC: 2437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.42
DANN	Benign	0.77
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs10224072; hg19: chr7-10318768;