6-25931349-A-G

Variant names:

• chr6-25931349-A-G
• rs199741
• ENST00000812771.1:n.80+2110A>G

Variant summary

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

The ENST00000812771.1(ENSG00000305751):​n.80+2110A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.81 in 151,906 control chromosomes in the GnomAD database, including 50,276 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 0.81 (50276 hom., cov: 29)
• Consequence: ENSG00000305751 ENST00000812771.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.581
• Publications: 10 publications found

Genes affected

ENSG00000305751 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.918 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
ENSG00000305751	ENST00000812771.1	n.80+2110A>G		intron_variant	Intron 1 of 2
ENSG00000305751	ENST00000812772.1	n.80+2110A>G		intron_variant	Intron 1 of 1
ENSG00000305751	ENST00000812773.1	n.73+2110A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.810 AC: 122953 AN: 151788 Hom.: 50229 Cov.: 29

Gnomad AFR AF: 0.926

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.810 AC: 123052 AN: 151906 Hom.: 50276 Cov.: 29 AF XY: 0.808 AC XY: 60023 AN XY: 74246

African (AFR) AF: 0.926 AC: 38373 AN: 41430

American (AMR) AF: 0.763 AC: 11634 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.747 AC: 2589 AN: 3466

East Asian (EAS) AF: 0.873 AC: 4501 AN: 5154

South Asian (SAS) AF: 0.717 AC: 3449 AN: 4812

European-Finnish (FIN) AF: 0.770 AC: 8117 AN: 10542

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.763 AC: 51835 AN: 67946

Other (OTH) AF: 0.808 AC: 1697 AN: 2100

Alfa AF: 0.776 Hom.: 202527

Bravo AF: 0.818

Asia WGS AF: 0.777 AC: 2704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.48
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs199741; hg19: chr6-25931577;