1-169716304-C-G

Variant names:

• chr1-169716304-C-G
• rs6693963
• ENST00000498289.5:n.851+32372C>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+32372C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,134 control chromosomes in the GnomAD database, including 1,521 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 0.14 (1521 hom., cov: 32)
• Consequence: FIRRM ENST00000498289.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.743
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.181 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FIRRM	ENST00000498289.5	TSL:2	n.851+32372C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20986 AN: 152016 Hom.: 1522 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.0612

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.138 AC: 20999 AN: 152134 Hom.: 1521 Cov.: 32 AF XY: 0.139 AC XY: 10334 AN XY: 74378

African (AFR) AF: 0.122 AC: 5058 AN: 41502

American (AMR) AF: 0.175 AC: 2671 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 574 AN: 3472

East Asian (EAS) AF: 0.0616 AC: 318 AN: 5164

South Asian (SAS) AF: 0.191 AC: 922 AN: 4820

European-Finnish (FIN) AF: 0.127 AC: 1347 AN: 10600

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9614 AN: 67994

Other (OTH) AF: 0.143 AC: 302 AN: 2114

Alfa AF: 0.0650 Hom.: 90

Bravo AF: 0.138

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.58
DANN	Benign	0.72
PhyloP100		-0.74

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6693963;

hg19: chr1-169685445;