ENST00000498289.5:n.851+37676A>G

Variant names:

• chr1-169721608-A-G
• rs12038818
• ENST00000498289.5:n.851+37676A>G

Variant summary

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

The ENST00000498289.5(FIRRM):​n.851+37676A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0677 in 152,038 control chromosomes in the GnomAD database, including 410 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 0.068 (410 hom., cov: 31)
• Consequence: FIRRM ENST00000498289.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.260
• Publications: 6 publications found

Genes affected

FIRRM (HGNC:25565): (FIGNL1 interacting regulator of recombination and mitosis)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FIRRM	ENST00000498289.5	n.851+37676A>G		intron_variant	Intron 3 of 28	2

Frequencies

GnomAD3 genomes AF: 0.0676 AC: 10276 AN: 151920 Hom.: 409 Cov.: 31

Gnomad AFR AF: 0.0790

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0482

Gnomad ASJ AF: 0.0890

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.0603

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0526

Gnomad OTH AF: 0.0766

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

GnomAD4 genome AF: 0.0677 AC: 10286 AN: 152038 Hom.: 410 Cov.: 31 AF XY: 0.0709 AC XY: 5271 AN XY: 74326

African (AFR) AF: 0.0791 AC: 3278 AN: 41428

American (AMR) AF: 0.0482 AC: 736 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0890 AC: 309 AN: 3470

East Asian (EAS) AF: 0.109 AC: 564 AN: 5170

South Asian (SAS) AF: 0.196 AC: 945 AN: 4810

European-Finnish (FIN) AF: 0.0603 AC: 638 AN: 10578

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0526 AC: 3574 AN: 67982

Other (OTH) AF: 0.0762 AC: 161 AN: 2112

Alfa AF: 0.0561 Hom.: 131

Bravo AF: 0.0651

Asia WGS AF: 0.170 AC: 592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.73
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs12038818; hg19: chr1-169690749;