6-14005790-A-G

Variant names:

• chr6-14005790-A-G
• rs1555051
• ENST00000427011.1:n.62-787A>G

Variant summary

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

The ENST00000427011.1(ENSG00000233981):​n.62-787A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 152,076 control chromosomes in the GnomAD database, including 9,522 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 0.35 (9522 hom., cov: 32)
• Consequence: ENSG00000233981 ENST00000427011.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45
• Publications: 8 publications found

Genes affected

ENSG00000233981 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000427011.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000233981	ENST00000427011.1	TSL:3	n.62-787A>G		intron	N/A
	ENSG00000233981	ENST00000814313.1		n.45-787A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52781 AN: 151960 Hom.: 9517 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.365

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.347 AC: 52805 AN: 152076 Hom.: 9522 Cov.: 32 AF XY: 0.348 AC XY: 25868 AN XY: 74338

African (AFR) AF: 0.241 AC: 9988 AN: 41500

American (AMR) AF: 0.386 AC: 5896 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1342 AN: 3472

East Asian (EAS) AF: 0.395 AC: 2040 AN: 5166

South Asian (SAS) AF: 0.283 AC: 1361 AN: 4808

European-Finnish (FIN) AF: 0.423 AC: 4470 AN: 10560

Middle Eastern (MID) AF: 0.383 AC: 111 AN: 290

European-Non Finnish (NFE) AF: 0.391 AC: 26551 AN: 67978

Other (OTH) AF: 0.378 AC: 799 AN: 2112

Alfa AF: 0.382 Hom.: 34506

Bravo AF: 0.338

Asia WGS AF: 0.368 AC: 1279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.16
DANN	Benign	0.33
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs1555051; hg19: chr6-14006021;