chr11-73984800-C-T

Variant names:

• chr11-73984800-C-T
• rs649446
• ENST00000660751.1:n.1352C>T

Variant summary

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

The ENST00000660751.1(ENSG00000287425):​n.1352C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,146 control chromosomes in the GnomAD database, including 3,699 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 0.22 (3699 hom., cov: 32)
• Consequence: ENSG00000287425 ENST00000660751.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.695
• Publications: 8 publications found

Genes affected

ENSG00000287425 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000660751.1. 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
	ENSG00000287425	ENST00000660751.1		n.1352C>T		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32879 AN: 152026 Hom.: 3699 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.216 AC: 32899 AN: 152146 Hom.: 3699 Cov.: 32 AF XY: 0.218 AC XY: 16200 AN XY: 74370

African (AFR) AF: 0.269 AC: 11146 AN: 41484

American (AMR) AF: 0.174 AC: 2661 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 734 AN: 3468

East Asian (EAS) AF: 0.285 AC: 1476 AN: 5178

South Asian (SAS) AF: 0.234 AC: 1129 AN: 4820

European-Finnish (FIN) AF: 0.206 AC: 2184 AN: 10582

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12924 AN: 68010

Other (OTH) AF: 0.212 AC: 449 AN: 2116

Alfa AF: 0.204 Hom.: 3890

Bravo AF: 0.215

Asia WGS AF: 0.239 AC: 831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	3.6
DANN	Benign	0.80
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs649446; hg19: chr11-73695845;