7-13861466-C-T

Variant names:

• chr7-13861466-C-T
• rs10282101
• ENST00000654062.1:n.483+170G>A

Variant summary

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

The ENST00000654062.1(ENSG00000224330):​n.483+170G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 152,054 control chromosomes in the GnomAD database, including 21,195 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 0.53 (21195 hom., cov: 33)
• Consequence: ENSG00000224330 ENST00000654062.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.403
• Publications: 3 publications found

Genes affected

ENSG00000224330 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654062.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000224330	ENST00000654062.1		n.483+170G>A		intron	N/A
	ENSG00000224330	ENST00000835227.1		n.95-2443G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79840 AN: 151936 Hom.: 21164 Cov.: 33

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.526 AC: 79927 AN: 152054 Hom.: 21195 Cov.: 33 AF XY: 0.526 AC XY: 39082 AN XY: 74346

African (AFR) AF: 0.578 AC: 23975 AN: 41472

American (AMR) AF: 0.509 AC: 7784 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1659 AN: 3470

East Asian (EAS) AF: 0.401 AC: 2068 AN: 5160

South Asian (SAS) AF: 0.546 AC: 2635 AN: 4826

European-Finnish (FIN) AF: 0.548 AC: 5786 AN: 10560

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.503 AC: 34209 AN: 67966

Other (OTH) AF: 0.526 AC: 1110 AN: 2110

Alfa AF: 0.514 Hom.: 2520

Bravo AF: 0.523

Asia WGS AF: 0.538 AC: 1875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.5
DANN	Benign	0.29
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs10282101; hg19: chr7-13901091;