rs7531806

Variant names:

• chr1-169681903-G-A
• rs7531806
• ENST00000498289.5:n.518-1566G>A

Variant summary

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

The ENST00000498289.5(FIRRM):​n.518-1566G>A variant causes a intron 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: FIRRM ENST00000498289.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.510
• Publications: 18 publications found

Genes affected

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

LOC107985745 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC107985745	XR_007066727.1	n.193-1566G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FIRRM	ENST00000498289.5	n.518-1566G>A		intron_variant	Intron 1 of 28	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

African (AFR) AF: 0.740 AC: 30679 AN: 41434

American (AMR) AF: 0.492 AC: 7512 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2158 AN: 3466

East Asian (EAS) AF: 0.428 AC: 2215 AN: 5172

South Asian (SAS) AF: 0.505 AC: 2426 AN: 4808

European-Finnish (FIN) AF: 0.553 AC: 5818 AN: 10524

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.564 AC: 38352 AN: 67952

Other (OTH) AF: 0.600 AC: 1264 AN: 2106

Alfa AF: 0.575 Hom.: 101318

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
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs7531806; hg19: chr1-169651044;