11-72181445-T-C

Variant names:

• chr11-72181445-T-C
• rs3887687
• ENST00000378140.3:n.419+17068A>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000378140.3(ENSG00000204971):​n.419+17068A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.45 (7 hom., cov: 43)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000204971 ENST00000378140.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 2 publications found

Genes affected

ENSG00000204971 (HGNC:58347):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

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.419+17068A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000204971	ENST00000378140.3	TSL:3	n.419+17068A>G		intron	N/A
	ENSG00000204971	ENST00000824615.1		n.218-18066A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.455 AC: 54346 AN: 119570 Hom.: 4 Cov.: 43

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.467

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.455 AC: 54392 AN: 119672 Hom.: 7 Cov.: 43 AF XY: 0.453 AC XY: 26533 AN XY: 58522

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.370 AC: 10822 AN: 29260

American (AMR) AF: 0.485 AC: 6210 AN: 12814

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1353 AN: 2810

East Asian (EAS) AF: 0.443 AC: 1630 AN: 3680

South Asian (SAS) AF: 0.461 AC: 1664 AN: 3608

European-Finnish (FIN) AF: 0.475 AC: 4137 AN: 8716

Middle Eastern (MID) AF: 0.473 AC: 105 AN: 222

European-Non Finnish (NFE) AF: 0.487 AC: 27297 AN: 56102

Other (OTH) AF: 0.467 AC: 753 AN: 1612

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.336 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.88
DANN	Benign	0.85
PhyloP100		-1.7

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3887687;

hg19: chr11-71892489;

COSMIC: COSV65379560;