rs16976820

Positions:

• chr15-56201697-G-A
• chr15-56201697-G-C

Variant summary

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

The NM_022841.7(RFX7):​c.162-22394C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.067 in 152,162 control chromosomes in the GnomAD database, including 457 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 0.067 (457 hom., cov: 32)
• Consequence: RFX7 NM_022841.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RFX7	NM_022841.7	c.162-22394C>T		intron_variant		ENST00000559447.8	NP_073752.6
RFX7	NM_001368073.2	c.-97+41428C>T		intron_variant			NP_001355002.1
RFX7	NM_001370561.1	c.162-22394C>T		intron_variant			NP_001357490.1
RFX7	XM_047432948.1	c.162-22394C>T		intron_variant			XP_047288904.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RFX7	ENST00000559447.8	c.162-22394C>T		intron_variant		5	NM_022841.7	ENSP00000453281	P1
RFX7	ENST00000673997.1	c.-97+41428C>T		intron_variant				ENSP00000501278
RFX7	ENST00000674082.1	c.-130-22394C>T		intron_variant				ENSP00000501248

Frequencies

GnomAD3 genomes AF: 0.0670 AC: 10181 AN: 152044 Hom.: 457 Cov.: 32

Gnomad AFR AF: 0.0201

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0268

Gnomad EAS AF: 0.00347

Gnomad SAS AF: 0.0276

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0887

Gnomad OTH AF: 0.0603

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

GnomAD4 genome AF: 0.0670 AC: 10196 AN: 152162 Hom.: 457 Cov.: 32 AF XY: 0.0671 AC XY: 4991 AN XY: 74392

Gnomad4 AFR AF: 0.0202

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.0268

Gnomad4 EAS AF: 0.00347

Gnomad4 SAS AF: 0.0265

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.0887

Gnomad4 OTH AF: 0.0616

Alfa AF: 0.0367 Hom.: 29

Bravo AF: 0.0637

Asia WGS AF: 0.0540 AC: 188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.36
DANN	Benign	0.64

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: rs16976820; hg19: chr15-56493895;