rs6924808

chr6-97910699-G-A

Variant summary

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

The ENST00000656098.1(ENSG00000271860):n.1255-58707G>A variant causes a intron, non coding transcript 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: ENST00000656098.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000656098.1	n.1255-58707G>A		intron_variant, non_coding_transcript_variant

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;