rs4656704

chr1-169719087-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000498289.5(FIRRM):n.851+35155A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 151,828 control chromosomes in the GnomAD database, including 6,847 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 0.30 (6847 hom., cov: 31)
• Consequence: FIRRM ENST00000498289.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.644

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FIRRM	ENST00000498289.5	n.851+35155A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44907 AN: 151710 Hom.: 6823 Cov.: 31

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.296 AC: 44983 AN: 151828 Hom.: 6847 Cov.: 31 AF XY: 0.299 AC XY: 22165 AN XY: 74188

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.321

Alfa AF: 0.283 Hom.: 977

Bravo AF: 0.302

Asia WGS AF: 0.378 AC: 1315 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	0.47
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4656704; hg19: chr1-169688228;