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. The variant received -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
• Publications: 4 publications found

Genes affected

ENSG00000233539 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000487094.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000233539	ENST00000469937.2	TSL:5	n.104-31901T>C		intron	N/A
	ENSG00000233539	ENST00000487094.1	TSL:3	n.110+34872T>C		intron	N/A

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

African (AFR) AF: 0.236 AC: 9784 AN: 41498

American (AMR) AF: 0.196 AC: 2994 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1047 AN: 3460

East Asian (EAS) AF: 0.321 AC: 1642 AN: 5108

South Asian (SAS) AF: 0.172 AC: 827 AN: 4812

European-Finnish (FIN) AF: 0.171 AC: 1812 AN: 10586

Middle Eastern (MID) AF: 0.297 AC: 86 AN: 290

European-Non Finnish (NFE) AF: 0.243 AC: 16483 AN: 67968

Other (OTH) AF: 0.245 AC: 518 AN: 2114

Alfa AF: 0.144 Hom.: 329

Bravo AF: 0.238

Asia WGS AF: 0.214 AC: 746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.1
DANN	Benign	0.64
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs856548; hg19: chr7-46764468;