rs580595

Variant names:

• chr6-83486032-A-G
• rs580595
• ENST00000738470.1:n.160+1653T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-83486032-A-G
• chr6-83486032-A-T

Variant summary

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

The ENST00000738470.1(ENSG00000296350):​n.160+1653T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.825 in 152,080 control chromosomes in the GnomAD database, including 52,074 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 0.82 (52074 hom., cov: 31)
• Consequence: ENSG00000296350 ENST00000738470.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395
• Publications: 3 publications found

Genes affected

ENSG00000296350 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 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
ENSG00000296350	ENST00000738470.1	n.160+1653T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.825 AC: 125333 AN: 151962 Hom.: 52009 Cov.: 31

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.887

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.779

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.825 AC: 125458 AN: 152080 Hom.: 52074 Cov.: 31 AF XY: 0.828 AC XY: 61514 AN XY: 74332

African (AFR) AF: 0.899 AC: 37302 AN: 41500

American (AMR) AF: 0.839 AC: 12824 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2537 AN: 3466

East Asian (EAS) AF: 0.944 AC: 4870 AN: 5160

South Asian (SAS) AF: 0.887 AC: 4274 AN: 4820

European-Finnish (FIN) AF: 0.785 AC: 8289 AN: 10558

Middle Eastern (MID) AF: 0.630 AC: 184 AN: 292

European-Non Finnish (NFE) AF: 0.779 AC: 52955 AN: 67986

Other (OTH) AF: 0.795 AC: 1678 AN: 2112

Alfa AF: 0.816 Hom.: 6192

Bravo AF: 0.827

Asia WGS AF: 0.898 AC: 3123 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	0.53
DANN	Benign	0.64
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs580595; hg19: chr6-84195751;