rs11599672

Variant names:

• chr10-93993019-T-G
• rs11599672
• ENST00000756959.1:n.166-201T>G

Variant summary

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

The ENST00000756959.1(ENSG00000298616):​n.166-201T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,046 control chromosomes in the GnomAD database, including 4,004 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 0.21 (4004 hom., cov: 32)
• Consequence: ENSG00000298616 ENST00000756959.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.556
• Publications: 6 publications found

Genes affected

ENSG00000298616 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000756959.1. 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
	ENSG00000298616	ENST00000756959.1		n.166-201T>G		intron	N/A
	ENSG00000298616	ENST00000756960.1		n.447-201T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31902 AN: 151928 Hom.: 4004 Cov.: 32

Gnomad AFR AF: 0.0724

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.210 AC: 31899 AN: 152046 Hom.: 4004 Cov.: 32 AF XY: 0.208 AC XY: 15425 AN XY: 74308

African (AFR) AF: 0.0723 AC: 2999 AN: 41500

American (AMR) AF: 0.257 AC: 3926 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 886 AN: 3472

East Asian (EAS) AF: 0.267 AC: 1379 AN: 5172

South Asian (SAS) AF: 0.201 AC: 965 AN: 4800

European-Finnish (FIN) AF: 0.222 AC: 2342 AN: 10546

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18678 AN: 67946

Other (OTH) AF: 0.200 AC: 424 AN: 2116

Alfa AF: 0.250 Hom.: 1981

Bravo AF: 0.209

Asia WGS AF: 0.214 AC: 746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.4
DANN	Benign	0.68
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs11599672; hg19: chr10-95752776;