rs856548

Positions:

• 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, non coding transcript 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: ENST00000487094.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000487094.1	n.110+34872T>C		intron_variant, non_coding_transcript_variant		3
	ENST00000469937.2	n.104-31901T>C		intron_variant, non_coding_transcript_variant		5

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;