rs6427212

Positions:

• chr1-169719900-G-A
• chr1-169719900-G-C

Variant summary

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

The ENST00000498289.5(FIRRM):​n.851+35968G>A 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 0.188 in 152,010 control chromosomes in the GnomAD database, including 2,953 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 0.19 (2953 hom., cov: 31)
• Consequence: FIRRM ENST00000498289.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.241 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+35968G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28501 AN: 151892 Hom.: 2941 Cov.: 31

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.188 AC: 28560 AN: 152010 Hom.: 2953 Cov.: 31 AF XY: 0.190 AC XY: 14142 AN XY: 74308

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.212

Alfa AF: 0.162 Hom.: 378

Bravo AF: 0.199

Asia WGS AF: 0.252 AC: 875 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.5
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6427212; hg19: chr1-169689041;