rs4957028

chr5-361582-C-T

Variant summary

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

The NM_001377236.1(AHRR):c.244+7671C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 151,994 control chromosomes in the GnomAD database, including 19,933 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 0.51 (19933 hom., cov: 33)
• Consequence: AHRR NM_001377236.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.86

Genes affected

AHRR (HGNC:346): (aryl hydrocarbon receptor repressor) The protein encoded by this gene participates in the aryl hydrocarbon receptor (AhR) signaling cascade, which mediates dioxin toxicity, and is involved in regulation of cell growth and differentiation. It functions as a feedback modulator by repressing AhR-dependent gene expression. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Jun 2011]

PDCD6-AHRR (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AHRR	NM_001377236.1	c.244+7671C>T		intron_variant		ENST00000684583.1
PDCD6-AHRR	NR_165159.2	n.537+7671C>T		intron_variant, non_coding_transcript_variant
AHRR	NM_001377239.1	c.244+7671C>T		intron_variant
PDCD6-AHRR	NR_165163.2	n.537+7671C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AHRR	ENST00000684583.1	c.244+7671C>T		intron_variant			NM_001377236.1	P1

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77219 AN: 151876 Hom.: 19926 Cov.: 33

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.508 AC: 77256 AN: 151994 Hom.: 19933 Cov.: 33 AF XY: 0.505 AC XY: 37495 AN XY: 74302

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.486

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.525

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.506

Alfa AF: 0.531 Hom.: 9796

Bravo AF: 0.505

Asia WGS AF: 0.402 AC: 1399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.24
Dann	Benign	0.54

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: rs4957028; hg19: chr5-361697;