rs4410790

Positions:

• chr7-17244953-T-C

Variant summary

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

The ENST00000643090.1(ENSG00000237773):​n.306+14299A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.541 in 151,920 control chromosomes in the GnomAD database, including 23,243 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 0.54 (23243 hom., cov: 31)
• Consequence: ENST00000643090.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264

Genes affected

(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 (NFE) allele frequency at 95% confidence interval = 0.621 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927609	XR_007060234.1	n.922+14299A>G		intron_variant, non_coding_transcript_variant
LOC101927609	XR_007060235.1	n.786+14299A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000643090.1	n.306+14299A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.542 AC: 82207 AN: 151802 Hom.: 23226 Cov.: 31

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.541 AC: 82252 AN: 151920 Hom.: 23243 Cov.: 31 AF XY: 0.539 AC XY: 40003 AN XY: 74264

Gnomad4 AFR AF: 0.455

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.692

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.548

Alfa AF: 0.604 Hom.: 39903

Bravo AF: 0.517

Asia WGS AF: 0.450 AC: 1557 AN: 3466

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	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4410790; hg19: chr7-17284577;