11-72180140-A-G

Variant names:

• chr11-72180140-A-G
• rs12361490
• ENST00000378140.3:n.420-16761T>C

Variant summary

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

The ENST00000378140.3(ENSG00000204971):​n.420-16761T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,096 control chromosomes in the GnomAD database, including 5,263 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 0.24 (5263 hom., cov: 32)
• Consequence: ENSG00000204971 ENST00000378140.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483
• Publications: 5 publications found

Genes affected

ENSG00000204971 (HGNC:58347):

ENSG00000307242 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000378140.3. 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
	FOLR1-AS1	NR_199595.1		n.420-16761T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000204971	ENST00000378140.3	TSL:3	n.420-16761T>C		intron	N/A
	ENSG00000204971	ENST00000824615.1		n.218-16761T>C		intron	N/A
	ENSG00000307242	ENST00000824701.1		n.1164+283A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35698 AN: 151978 Hom.: 5230 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.235 AC: 35769 AN: 152096 Hom.: 5263 Cov.: 32 AF XY: 0.239 AC XY: 17774 AN XY: 74348

African (AFR) AF: 0.408 AC: 16915 AN: 41466

American (AMR) AF: 0.173 AC: 2639 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 533 AN: 3470

East Asian (EAS) AF: 0.354 AC: 1830 AN: 5168

South Asian (SAS) AF: 0.288 AC: 1386 AN: 4814

European-Finnish (FIN) AF: 0.192 AC: 2035 AN: 10592

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.146 AC: 9931 AN: 67994

Other (OTH) AF: 0.200 AC: 422 AN: 2106

Alfa AF: 0.182 Hom.: 1005

Bravo AF: 0.238

Asia WGS AF: 0.361 AC: 1255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.37
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs12361490; hg19: chr11-71891184;