rs1632344

chr6-94171254-A-C

Variant summary

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

The ENST00000424506.1(ENSG00000231143):n.30+7305A>C 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 0.249 in 151,964 control chromosomes in the GnomAD database, including 5,005 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 0.25 (5005 hom., cov: 32)
• Consequence: ENST00000424506.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000424506.1	n.30+7305A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37796 AN: 151846 Hom.: 4982 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.249 AC: 37864 AN: 151964 Hom.: 5005 Cov.: 32 AF XY: 0.245 AC XY: 18192 AN XY: 74264

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.257

Alfa AF: 0.237 Hom.: 751

Bravo AF: 0.247

Asia WGS AF: 0.185 AC: 645 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.6
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1632344; hg19: chr6-94880972;