rs6961860

chr7-17045697-C-T

Variant summary

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

The XR_007060239.1(LOC124901595):n.4831G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 151,800 control chromosomes in the GnomAD database, including 12,635 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 0.40 (12635 hom., cov: 32)
• Consequence: LOC124901595 XR_007060239.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104

Genes affected

LOC124901595 (HGNC:):

AHR (HGNC:348): (aryl hydrocarbon receptor) The protein encoded by this gene is a ligand-activated helix-loop-helix transcription factor involved in the regulation of biological responses to planar aromatic hydrocarbons. This receptor has been shown to regulate xenobiotic-metabolizing enzymes such as cytochrome P450. Before ligand binding, the encoded protein is sequestered in the cytoplasm; upon ligand binding, this protein moves to the nucleus and stimulates transcription of target genes. [provided by RefSeq, Sep 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901595	XR_007060239.1	n.4831G>A		non_coding_transcript_exon_variant	1/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000643090.1	n.307-73951G>A		intron_variant, non_coding_transcript_variant
AHR	ENST00000645559.1	n.30+129309C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61109 AN: 151680 Hom.: 12625 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.403 AC: 61161 AN: 151800 Hom.: 12635 Cov.: 32 AF XY: 0.404 AC XY: 29995 AN XY: 74182

Gnomad4 AFR AF: 0.477

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.432

Gnomad4 SAS AF: 0.401

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.388

Alfa AF: 0.361 Hom.: 16345

Bravo AF: 0.416

Asia WGS AF: 0.419 AC: 1459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.0
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6961860; hg19: chr7-17085321;