rs1632344

Variant names:

• chr6-94171254-A-C
• rs1632344
• ENST00000424506.1:n.30+7305A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000424506.1(ENSG00000231143):​n.30+7305A>C variant causes a intron 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: ENSG00000231143 ENST00000424506.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939
• Publications: 1 publications found

Genes affected

ENSG00000231143 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231143	ENST00000424506.1	n.30+7305A>C		intron_variant	Intron 1 of 1	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

African (AFR) AF: 0.310 AC: 12826 AN: 41434

American (AMR) AF: 0.184 AC: 2814 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 860 AN: 3468

East Asian (EAS) AF: 0.106 AC: 546 AN: 5156

South Asian (SAS) AF: 0.209 AC: 1008 AN: 4828

European-Finnish (FIN) AF: 0.243 AC: 2575 AN: 10578

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16205 AN: 67928

Other (OTH) AF: 0.257 AC: 542 AN: 2112

Alfa AF: 0.239 Hom.: 785

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
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs1632344; hg19: chr6-94880972;