rs6906804

Variant names:

• chr6-1490347-G-A
• rs6906804
• ENST00000808840.1:n.283+404G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000808840.1(ENSG00000305114):​n.283+404G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,056 control chromosomes in the GnomAD database, including 5,596 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 0.26 (5596 hom., cov: 32)
• Consequence: ENSG00000305114 ENST00000808840.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.932
• Publications: 1 publications found

Genes affected

ENSG00000305114 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374883	XR_007059402.1	n.266-351G>A		intron_variant	Intron 2 of 2
LOC102723944	XR_427861.4	n.347+12104C>T		intron_variant	Intron 3 of 6
LOC105374883	XR_926387.3	n.265+404G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305114	ENST00000808840.1	n.283+404G>A		intron_variant	Intron 2 of 2
ENSG00000272279	ENST00000808970.1	n.225+12104C>T		intron_variant	Intron 2 of 2
ENSG00000272279	ENST00000808971.1	n.180+12104C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.257 AC: 38985 AN: 151938 Hom.: 5572 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.257 AC: 39061 AN: 152056 Hom.: 5596 Cov.: 32 AF XY: 0.263 AC XY: 19540 AN XY: 74316

African (AFR) AF: 0.303 AC: 12577 AN: 41456

American (AMR) AF: 0.403 AC: 6163 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 583 AN: 3472

East Asian (EAS) AF: 0.317 AC: 1633 AN: 5156

South Asian (SAS) AF: 0.381 AC: 1836 AN: 4824

European-Finnish (FIN) AF: 0.213 AC: 2251 AN: 10574

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13155 AN: 67976

Other (OTH) AF: 0.282 AC: 594 AN: 2108

Alfa AF: 0.227 Hom.: 11724

Bravo AF: 0.274

Asia WGS AF: 0.381 AC: 1325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	8.5
DANN	Benign	0.34
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs6906804; hg19: chr6-1490582; COSMIC: COSV70073422;