rs7105630

Variant names:

• chr11-103533134-T-C
• rs7105630
• ENST00000827359.1:n.120-2959A>G

Variant summary

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

The ENST00000827359.1(ENSG00000307600):​n.120-2959A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 152,034 control chromosomes in the GnomAD database, including 29,658 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 0.60 (29658 hom., cov: 32)
• Consequence: ENSG00000307600 ENST00000827359.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.469
• Publications: 3 publications found

Genes affected

ENSG00000307600 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827359.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307600	ENST00000827359.1		n.120-2959A>G		intron	N/A
	ENSG00000307600	ENST00000827360.1		n.92+3275A>G		intron	N/A
	ENSG00000307600	ENST00000827363.1		n.92-2959A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91594 AN: 151916 Hom.: 29652 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.603 AC: 91627 AN: 152034 Hom.: 29658 Cov.: 32 AF XY: 0.606 AC XY: 44982 AN XY: 74280

African (AFR) AF: 0.342 AC: 14171 AN: 41434

American (AMR) AF: 0.698 AC: 10667 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2476 AN: 3472

East Asian (EAS) AF: 0.734 AC: 3782 AN: 5154

South Asian (SAS) AF: 0.662 AC: 3193 AN: 4826

European-Finnish (FIN) AF: 0.685 AC: 7245 AN: 10574

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.705 AC: 47937 AN: 67976

Other (OTH) AF: 0.639 AC: 1348 AN: 2110

Alfa AF: 0.681 Hom.: 148243

Bravo AF: 0.596

Asia WGS AF: 0.667 AC: 2320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.7
DANN	Benign	0.79
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs7105630; hg19: chr11-103403862;