6-29861195-A-G

Variant names:

• chr6-29861195-A-G
• rs9258750
• ENST00000647952.1:n.2063-3757T>C

Variant summary

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

The ENST00000647952.1(ENSG00000290870):​n.2063-3757T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 151,988 control chromosomes in the GnomAD database, including 5,959 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 0.27 (5959 hom., cov: 31)
• Consequence: ENSG00000290870 ENST00000647952.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.413
• Publications: 11 publications found

Genes affected

ENSG00000290870 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 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

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
	ENSG00000290870	ENST00000647952.1		n.2063-3757T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40599 AN: 151870 Hom.: 5948 Cov.: 31

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.267 AC: 40632 AN: 151988 Hom.: 5959 Cov.: 31 AF XY: 0.268 AC XY: 19924 AN XY: 74298

African (AFR) AF: 0.389 AC: 16105 AN: 41406

American (AMR) AF: 0.328 AC: 5004 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 814 AN: 3468

East Asian (EAS) AF: 0.244 AC: 1262 AN: 5180

South Asian (SAS) AF: 0.259 AC: 1251 AN: 4826

European-Finnish (FIN) AF: 0.190 AC: 2003 AN: 10554

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13346 AN: 67968

Other (OTH) AF: 0.285 AC: 601 AN: 2110

Alfa AF: 0.259 Hom.: 3747

Bravo AF: 0.286

Asia WGS AF: 0.323 AC: 1124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.3
DANN	Benign	0.80
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs9258750; hg19: chr6-29828972;