rs7531806

Positions:

• chr1-169681903-G-A

Variant summary

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

The XR_007066727.1(LOC107985745):​n.193-1566G>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 0.6 in 151,920 control chromosomes in the GnomAD database, including 28,123 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 0.60 (28123 hom., cov: 31)
• Consequence: LOC107985745 XR_007066727.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.510

Genes affected

LOC107985745 (HGNC:):

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985745	XR_007066727.1	n.193-1566G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FIRRM	ENST00000498289.5	n.518-1566G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.600 AC: 91047 AN: 151802 Hom.: 28085 Cov.: 31

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.600 AC: 91133 AN: 151920 Hom.: 28123 Cov.: 31 AF XY: 0.593 AC XY: 44035 AN XY: 74256

Gnomad4 AFR AF: 0.740

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.623

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.553

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.600

Alfa AF: 0.569 Hom.: 41211

Bravo AF: 0.602

Asia WGS AF: 0.495 AC: 1725 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	10
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7531806; hg19: chr1-169651044;