7-16065520-T-C

Variant names:

• chr7-16065520-T-C
• rs10487907
• ENST00000779607.1:n.118-230T>C

Variant summary

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

The ENST00000779607.1(ENSG00000301543):​n.118-230T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0775 in 152,154 control chromosomes in the GnomAD database, including 728 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 0.077 (728 hom., cov: 32)
• Consequence: ENSG00000301543 ENST00000779607.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.788
• Publications: 2 publications found

Genes affected

ENSG00000301543 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.296 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
ENSG00000301543	ENST00000779607.1	n.118-230T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0773 AC: 11759 AN: 152036 Hom.: 723 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0578

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.0740

Gnomad FIN AF: 0.0226

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0416

Gnomad OTH AF: 0.0891

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

GnomAD4 genome AF: 0.0775 AC: 11791 AN: 152154 Hom.: 728 Cov.: 32 AF XY: 0.0774 AC XY: 5760 AN XY: 74386

African (AFR) AF: 0.121 AC: 5027 AN: 41532

American (AMR) AF: 0.0577 AC: 881 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 629 AN: 3470

East Asian (EAS) AF: 0.309 AC: 1589 AN: 5150

South Asian (SAS) AF: 0.0751 AC: 362 AN: 4822

European-Finnish (FIN) AF: 0.0226 AC: 240 AN: 10614

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0416 AC: 2825 AN: 67982

Other (OTH) AF: 0.0900 AC: 190 AN: 2110

Alfa AF: 0.0157 Hom.: 5

Bravo AF: 0.0844

Asia WGS AF: 0.178 AC: 618 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.27
DANN	Benign	0.57
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs10487907; hg19: chr7-16105145;