rs1885659

Variant names:

• chr6-43797796-A-G
• rs1885659
• ENST00000719551.1:n.192+446A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-43797796-A-G
• chr6-43797796-A-T

Variant summary

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

The ENST00000719551.1(ENSG00000283573):​n.192+446A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.801 in 152,266 control chromosomes in the GnomAD database, including 49,329 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 0.80 (49329 hom., cov: 34)
• Consequence: ENSG00000283573 ENST00000719551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 7 publications found

Genes affected

ENSG00000283573 (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 (SAS) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375070	XR_007059588.1	n.192+446A>G		intron_variant	Intron 1 of 2
LOC105375070	XR_007059589.1	n.192+446A>G		intron_variant	Intron 1 of 2
LOC105375070	XR_926833.3	n.192+446A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283573	ENST00000719551.1	n.192+446A>G		intron_variant	Intron 1 of 2
ENSG00000283573	ENST00000719553.1	n.192+446A>G		intron_variant	Intron 1 of 2
ENSG00000283573	ENST00000719555.1	n.159+446A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.800 AC: 121772 AN: 152148 Hom.: 49265 Cov.: 34

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.840

Gnomad SAS AF: 0.940

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.796

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

GnomAD4 genome AF: 0.801 AC: 121897 AN: 152266 Hom.: 49329 Cov.: 34 AF XY: 0.800 AC XY: 59594 AN XY: 74452

African (AFR) AF: 0.923 AC: 38344 AN: 41560

American (AMR) AF: 0.742 AC: 11354 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.808 AC: 2807 AN: 3472

East Asian (EAS) AF: 0.840 AC: 4351 AN: 5180

South Asian (SAS) AF: 0.941 AC: 4549 AN: 4832

European-Finnish (FIN) AF: 0.716 AC: 7594 AN: 10604

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.739 AC: 50250 AN: 68004

Other (OTH) AF: 0.798 AC: 1684 AN: 2110

Alfa AF: 0.762 Hom.: 56171

Bravo AF: 0.803

Asia WGS AF: 0.885 AC: 3078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.79
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1885659; hg19: chr6-43765533;