rs6924808

Variant names:

• chr6-97910699-G-A
• rs6924808
• ENST00000606913.5:n.155+25044G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000606913.5(ENSG00000271860):​n.155+25044G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 151,962 control chromosomes in the GnomAD database, including 22,851 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 0.55 (22851 hom., cov: 31)
• Consequence: ENSG00000271860 ENST00000606913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600

Genes affected

ENSG00000271860 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000271860	ENST00000606913.5	n.155+25044G>A		intron_variant	Intron 1 of 4	5
ENSG00000271860	ENST00000607823.5	n.207-58707G>A		intron_variant	Intron 2 of 6	5
ENSG00000271860	ENST00000653817.1	n.866+82493G>A		intron_variant	Intron 8 of 11

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82780 AN: 151844 Hom.: 22813 Cov.: 31

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.545 AC: 82879 AN: 151962 Hom.: 22851 Cov.: 31 AF XY: 0.551 AC XY: 40901 AN XY: 74268

Gnomad4 AFR AF: 0.600

Gnomad4 AMR AF: 0.539

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.675

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.511

Gnomad4 OTH AF: 0.545

Alfa AF: 0.531 Hom.: 10407

Bravo AF: 0.536

Asia WGS AF: 0.597 AC: 2075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.88
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6924808; hg19: chr6-98358575;