rs10518839

chr15-56192165-T-A

Variant summary

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

The NM_022841.7(RFX7):c.162-12862A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,104 control chromosomes in the GnomAD database, including 1,651 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 0.13 (1651 hom., cov: 31)
• Consequence: RFX7 NM_022841.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.997

Genes affected

RFX7 (HGNC:25777): (regulatory factor X7) RFX7 is a member of the regulatory factor X (RFX) family of transcription factors (see RFX1, MIM 600006) (Aftab et al., 2008 [PubMed 18673564]).[supplied by OMIM, Mar 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RFX7	NM_022841.7	c.162-12862A>T		intron_variant		ENST00000559447.8
RFX7	NM_001368073.2	c.-96-47682A>T		intron_variant
RFX7	NM_001370561.1	c.162-12862A>T		intron_variant
RFX7	XM_047432948.1	c.162-12862A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RFX7	ENST00000559447.8	c.162-12862A>T		intron_variant		5	NM_022841.7	P1
RFX7	ENST00000673997.1	c.-96-47682A>T		intron_variant
RFX7	ENST00000674082.1	c.-130-12862A>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19634 AN: 151986 Hom.: 1652 Cov.: 31

Gnomad AFR AF: 0.0868

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.0830

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.129 AC: 19645 AN: 152104 Hom.: 1651 Cov.: 31 AF XY: 0.133 AC XY: 9861 AN XY: 74340

Gnomad4 AFR AF: 0.0866

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.0830

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.162

Alfa AF: 0.116 Hom.: 159

Bravo AF: 0.130

Asia WGS AF: 0.316 AC: 1100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	10
Dann	Benign	0.73

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10518839; hg19: chr15-56484363;