rs649060

Variant names:

• chr11-72181857-G-C
• rs649060
• ENST00000378140.3:n.419+16656C>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+16656C>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 0.31 (0 hom., cov: 36)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000204971 ENST00000378140.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 1 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=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOLR1-AS1	NR_199595.1	n.419+16656C>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000204971	ENST00000378140.3	n.419+16656C>G		intron_variant	Intron 2 of 2	3
ENSG00000204971	ENST00000824615.1	n.218-18478C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.307 AC: 20138 AN: 65588 Hom.: 0 Cov.: 36

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.301

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: AS_VQSR;InbreedingCoeff AF: 0.307 AC: 20155 AN: 65670 Hom.: 0 Cov.: 36 AF XY: 0.307 AC XY: 10135 AN XY: 32980

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

African (AFR) AF: 0.239 AC: 4843 AN: 20274

American (AMR) AF: 0.363 AC: 2496 AN: 6884

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 442 AN: 1300

East Asian (EAS) AF: 0.203 AC: 441 AN: 2176

South Asian (SAS) AF: 0.263 AC: 534 AN: 2034

European-Finnish (FIN) AF: 0.311 AC: 1521 AN: 4888

Middle Eastern (MID) AF: 0.214 AC: 24 AN: 112

European-Non Finnish (NFE) AF: 0.353 AC: 9434 AN: 26746

Other (OTH) AF: 0.301 AC: 276 AN: 918

⚠️ 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: 0.345 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	8.4
DANN	Benign	0.63
PhyloP100		-0.055

Splicing

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

Other links and lift over

dbSNP: rs649060; hg19: chr11-71892901; COSMIC: COSV65379534;