1-169719900-G-A

Variant names:

• chr1-169719900-G-A
• rs6427212
• ENST00000498289.5:n.851+35968G>A

Variant summary

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

The ENST00000498289.5(FIRRM):​n.851+35968G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000498289.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FIRRM	ENST00000498289.5	TSL:2	n.851+35968G>A		intron	N/A

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

African (AFR) AF: 0.243 AC: 10053 AN: 41442

American (AMR) AF: 0.247 AC: 3768 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 616 AN: 3468

East Asian (EAS) AF: 0.252 AC: 1301 AN: 5164

South Asian (SAS) AF: 0.236 AC: 1137 AN: 4812

European-Finnish (FIN) AF: 0.172 AC: 1819 AN: 10586

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9214 AN: 67950

Other (OTH) AF: 0.212 AC: 448 AN: 2112

Alfa AF: 0.164 Hom.: 396

Bravo AF: 0.199

Asia WGS AF: 0.252 AC: 875 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.5
DANN	Benign	0.68
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs6427212; hg19: chr1-169689041;