chr15-56201697-G-A

Variant names:

• chr15-56201697-G-A
• rs16976820
• NM_022841.7:c.162-22394C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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]

RFX7 Gene-Disease associations (from GenCC):

• intellectual developmental disorder, autosomal dominant 71, with behavioral abnormalities

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022841.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RFX7	NM_022841.7	MANE Select	c.162-22394C>T		intron	N/A	NP_073752.6
	RFX7	NM_001370561.1		c.162-22394C>T		intron	N/A	NP_001357490.1
	RFX7	NM_001368073.2		c.-97+41428C>T		intron	N/A	NP_001355002.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RFX7	ENST00000559447.8	TSL:5 MANE Select	c.162-22394C>T		intron	N/A	ENSP00000453281.3
	RFX7	ENST00000673997.1		c.-97+41428C>T		intron	N/A	ENSP00000501278.1
	RFX7	ENST00000674082.1		c.-130-22394C>T		intron	N/A	ENSP00000501248.1

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

African (AFR) AF: 0.0202 AC: 838 AN: 41530

American (AMR) AF: 0.106 AC: 1619 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0268 AC: 93 AN: 3466

East Asian (EAS) AF: 0.00347 AC: 18 AN: 5180

South Asian (SAS) AF: 0.0265 AC: 128 AN: 4822

European-Finnish (FIN) AF: 0.119 AC: 1256 AN: 10564

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0887 AC: 6029 AN: 67994

Other (OTH) AF: 0.0616 AC: 130 AN: 2112

Alfa AF: 0.0360 Hom.: 30

Bravo AF: 0.0637

Asia WGS AF: 0.0540 AC: 188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.36
DANN	Benign	0.64
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs16976820; hg19: chr15-56493895;