rs1893008

Variant names:

• chr11-72183542-G-A
• rs1893008
• ENST00000378140.3:n.419+14971C>T

Variant summary

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

The ENST00000378140.3(ENSG00000204971):​n.419+14971C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.017 in 152,226 control chromosomes in the GnomAD database, including 42 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 0.017 (42 hom., cov: 32)
• Consequence: ENSG00000204971 ENST00000378140.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.76
• Publications: 3 publications found

Genes affected

ENSG00000204971 (HGNC:58347):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOLR1-AS1	NR_199595.1	n.419+14971C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000204971	ENST00000378140.3	n.419+14971C>T		intron_variant	Intron 2 of 2	3
ENSG00000204971	ENST00000824615.1	n.218-20163C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0169 AC: 2572 AN: 152108 Hom.: 40 Cov.: 32

Gnomad AFR AF: 0.0179

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0138

Gnomad ASJ AF: 0.0248

Gnomad EAS AF: 0.0756

Gnomad SAS AF: 0.0644

Gnomad FIN AF: 0.0135

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00942

Gnomad OTH AF: 0.0172

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

GnomAD4 genome AF: 0.0170 AC: 2585 AN: 152226 Hom.: 42 Cov.: 32 AF XY: 0.0186 AC XY: 1381 AN XY: 74436

African (AFR) AF: 0.0182 AC: 755 AN: 41520

American (AMR) AF: 0.0138 AC: 211 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0248 AC: 86 AN: 3472

East Asian (EAS) AF: 0.0756 AC: 390 AN: 5158

South Asian (SAS) AF: 0.0643 AC: 310 AN: 4822

European-Finnish (FIN) AF: 0.0135 AC: 143 AN: 10616

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00944 AC: 642 AN: 68028

Other (OTH) AF: 0.0166 AC: 35 AN: 2112

Alfa AF: 0.0139 Hom.: 4

Bravo AF: 0.0166

Asia WGS AF: 0.0500 AC: 175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.14
DANN	Benign	0.83
PhyloP100		-3.8
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1893008; hg19: chr11-71894586;