rs856548

Variant names:

• chr7-46724870-A-G
• rs856548
• ENST00000469937.2:n.104-31901T>C

Your query was ambiguous. Multiple possible variants found:

• chr7-46724870-A-G
• chr7-46724870-A-T

Variant summary

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

The ENST00000487094.1(ENSG00000233539):​n.110+34872T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,028 control chromosomes in the GnomAD database, including 4,345 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 0.23 (4345 hom., cov: 31)
• Consequence: ENSG00000233539 ENST00000487094.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205

Genes affected

ENSG00000233539 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.309 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
ENSG00000233539	ENST00000469937.2	n.104-31901T>C		intron_variant	Intron 1 of 2	5
ENSG00000233539	ENST00000487094.1	n.110+34872T>C		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35351 AN: 151910 Hom.: 4344 Cov.: 31

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.233 AC: 35381 AN: 152028 Hom.: 4345 Cov.: 31 AF XY: 0.229 AC XY: 16989 AN XY: 74304

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.245

Alfa AF: 0.140 Hom.: 308

Bravo AF: 0.238

Asia WGS AF: 0.214 AC: 746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.1
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs856548; hg19: chr7-46764468;