rs6092361

Variant names:

• chr20-56764564-G-A
• rs6092361
• ENST00000807007.1:n.74-14199G>A

Variant summary

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

The ENST00000807007.1(ENSG00000304895):​n.74-14199G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 151,832 control chromosomes in the GnomAD database, including 10,026 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 0.36 (10026 hom., cov: 33)
• Consequence: ENSG00000304895 ENST00000807007.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.582
• Publications: 3 publications found

Genes affected

ENSG00000304895 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807007.1. 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
	ENSG00000304895	ENST00000807007.1		n.74-14199G>A		intron	N/A
	ENSG00000304895	ENST00000807008.1		n.45-14199G>A		intron	N/A
	ENSG00000304895	ENST00000807009.1		n.109+13822G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54474 AN: 151716 Hom.: 10021 Cov.: 33

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.359 AC: 54511 AN: 151832 Hom.: 10026 Cov.: 33 AF XY: 0.356 AC XY: 26419 AN XY: 74202

African (AFR) AF: 0.422 AC: 17450 AN: 41316

American (AMR) AF: 0.302 AC: 4619 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1231 AN: 3458

East Asian (EAS) AF: 0.147 AC: 763 AN: 5174

South Asian (SAS) AF: 0.374 AC: 1799 AN: 4810

European-Finnish (FIN) AF: 0.352 AC: 3703 AN: 10520

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23803 AN: 67974

Other (OTH) AF: 0.354 AC: 747 AN: 2108

Alfa AF: 0.351 Hom.: 26049

Bravo AF: 0.353

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.41
DANN	Benign	0.88
PhyloP100		-0.58

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6092361;

hg19: chr20-55339620;