6-29866672-A-G

Variant names:

• chr6-29866672-A-G
• rs2734971

Variant summary

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

The variant allele was found at a frequency of 0.565 in 151,974 control chromosomes in the GnomAD database, including 24,937 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 0.57 (24937 hom., cov: 32)
• Consequence: LOC353009 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.74
• Publications: 20 publications found

Genes affected

LOC353009 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647952.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290870	ENST00000647952.1		n.2063-9234T>C		intron	N/A
	POLR1HASP	ENST00000849679.1		n.587-3846T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85809 AN: 151854 Hom.: 24893 Cov.: 32

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.565 AC: 85904 AN: 151974 Hom.: 24937 Cov.: 32 AF XY: 0.562 AC XY: 41767 AN XY: 74278

African (AFR) AF: 0.650 AC: 26942 AN: 41430

American (AMR) AF: 0.608 AC: 9283 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2382 AN: 3464

East Asian (EAS) AF: 0.519 AC: 2677 AN: 5154

South Asian (SAS) AF: 0.706 AC: 3397 AN: 4814

European-Finnish (FIN) AF: 0.343 AC: 3623 AN: 10572

Middle Eastern (MID) AF: 0.661 AC: 193 AN: 292

European-Non Finnish (NFE) AF: 0.525 AC: 35671 AN: 67948

Other (OTH) AF: 0.608 AC: 1285 AN: 2114

Alfa AF: 0.542 Hom.: 17122

Bravo AF: 0.586

Asia WGS AF: 0.672 AC: 2339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.62
DANN	Benign	0.30
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs2734971; hg19: chr6-29834449;