chr6-29702484-A-G

Variant names:

• chr6-29702484-A-G
• rs3129055
• ENST00000850325.1:n.220-5956A>G

Variant summary

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

The ENST00000850325.1(ENSG00000310484):​n.220-5956A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 152,102 control chromosomes in the GnomAD database, including 4,837 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 (4837 hom., cov: 33)
• Consequence: ENSG00000310484 ENST00000850325.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.242
• Publications: 62 publications found

Genes affected

ENSG00000310484 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000850325.1. 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
	ENSG00000310484	ENST00000850325.1		n.220-5956A>G		intron	N/A
	ENSG00000310484	ENST00000850326.1		n.202-5956A>G		intron	N/A
	ENSG00000310484	ENST00000850327.1		n.-232A>G		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37692 AN: 151984 Hom.: 4819 Cov.: 33

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.248 AC: 37733 AN: 152102 Hom.: 4837 Cov.: 33 AF XY: 0.244 AC XY: 18157 AN XY: 74362

African (AFR) AF: 0.230 AC: 9556 AN: 41476

American (AMR) AF: 0.279 AC: 4262 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 631 AN: 3464

East Asian (EAS) AF: 0.348 AC: 1798 AN: 5168

South Asian (SAS) AF: 0.335 AC: 1618 AN: 4830

European-Finnish (FIN) AF: 0.148 AC: 1570 AN: 10606

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17453 AN: 67960

Other (OTH) AF: 0.252 AC: 533 AN: 2112

Alfa AF: 0.256 Hom.: 14596

Bravo AF: 0.255

Asia WGS AF: 0.414 AC: 1442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.1
DANN	Benign	0.44
PhyloP100		-0.24

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3129055;

hg19: chr6-29670261;