2-215438330-A-G

Variant names:

• chr2-215438330-A-G
• rs3910516
• NR_187198.1:n.2031A>G

Variant summary

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

The NR_187198.1(FN1-DT):​n.2031A>G 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 0.785 in 150,142 control chromosomes in the GnomAD database, including 46,748 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 0.79 (46748 hom., cov: 26)
• Consequence: FN1-DT NR_187198.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• Publications: 5 publications found

Genes affected

FN1-DT (HGNC:55775): (FN1 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FN1-DT	NR_187198.1	n.2031A>G		non_coding_transcript_exon_variant	Exon 2 of 2
FN1-DT	NR_187199.1	n.1770A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.785 AC: 117841 AN: 150040 Hom.: 46710 Cov.: 26

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.779

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

GnomAD4 genome AF: 0.785 AC: 117923 AN: 150142 Hom.: 46748 Cov.: 26 AF XY: 0.787 AC XY: 57669 AN XY: 73238

African (AFR) AF: 0.869 AC: 35594 AN: 40946

American (AMR) AF: 0.777 AC: 11763 AN: 15148

Ashkenazi Jewish (ASJ) AF: 0.787 AC: 2725 AN: 3464

East Asian (EAS) AF: 0.924 AC: 4738 AN: 5128

South Asian (SAS) AF: 0.571 AC: 2727 AN: 4774

European-Finnish (FIN) AF: 0.809 AC: 7918 AN: 9788

Middle Eastern (MID) AF: 0.760 AC: 219 AN: 288

European-Non Finnish (NFE) AF: 0.738 AC: 49877 AN: 67610

Other (OTH) AF: 0.780 AC: 1629 AN: 2088

Alfa AF: 0.763 Hom.: 5240

Bravo AF: 0.793

Asia WGS AF: 0.701 AC: 2427 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.64
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs3910516; hg19: chr2-216303053;