6-6734789-G-A

Variant names:

• chr6-6734789-G-A
• rs1294404
• ENST00000648205.2:n.122+4120C>T

Variant summary

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

The ENST00000648205.2(ENSG00000226281):​n.122+4120C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 151,900 control chromosomes in the GnomAD database, including 32,617 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 0.64 (32617 hom., cov: 30)
• Consequence: ENSG00000226281 ENST00000648205.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366
• Publications: 7 publications found

Genes affected

ENSG00000226281 (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 (AFR) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648205.2. 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
	LOC101928004	NR_187687.1		n.486-22931C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226281	ENST00000648205.2		n.122+4120C>T		intron	N/A
	ENSG00000226281	ENST00000656346.2		n.119+4120C>T		intron	N/A
	ENSG00000226281	ENST00000666858.2		n.133+82C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97328 AN: 151782 Hom.: 32596 Cov.: 30

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.641 AC: 97382 AN: 151900 Hom.: 32617 Cov.: 30 AF XY: 0.630 AC XY: 46774 AN XY: 74222

African (AFR) AF: 0.816 AC: 33820 AN: 41434

American (AMR) AF: 0.527 AC: 8056 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2174 AN: 3464

East Asian (EAS) AF: 0.235 AC: 1210 AN: 5152

South Asian (SAS) AF: 0.408 AC: 1959 AN: 4800

European-Finnish (FIN) AF: 0.607 AC: 6397 AN: 10532

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41786 AN: 67920

Other (OTH) AF: 0.601 AC: 1269 AN: 2110

Alfa AF: 0.626 Hom.: 5961

Bravo AF: 0.641

Asia WGS AF: 0.327 AC: 1138 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	0.78
DANN	Benign	0.36
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs1294404; hg19: chr6-6735022;