rs1308020

Variant names:

• chr11-65730087-G-A
• rs1308020
• ENST00000744235.1:n.285-2232C>T

Variant summary

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

The ENST00000744235.1(ENSG00000297007):​n.285-2232C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 151,970 control chromosomes in the GnomAD database, including 6,399 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 0.28 (6399 hom., cov: 30)
• Consequence: ENSG00000297007 ENST00000744235.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• Publications: 14 publications found

Genes affected

ENSG00000297007 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000744235.1. 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
	ENSG00000297007	ENST00000744235.1		n.285-2232C>T		intron	N/A
	ENSG00000297007	ENST00000744236.1		n.250-2232C>T		intron	N/A
	ENSG00000297007	ENST00000744237.1		n.96-2232C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42963 AN: 151852 Hom.: 6399 Cov.: 30

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.283 AC: 42973 AN: 151970 Hom.: 6399 Cov.: 30 AF XY: 0.277 AC XY: 20553 AN XY: 74252

African (AFR) AF: 0.213 AC: 8812 AN: 41462

American (AMR) AF: 0.261 AC: 3975 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 961 AN: 3466

East Asian (EAS) AF: 0.249 AC: 1282 AN: 5158

South Asian (SAS) AF: 0.247 AC: 1190 AN: 4816

European-Finnish (FIN) AF: 0.248 AC: 2613 AN: 10554

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.339 AC: 23059 AN: 67950

Other (OTH) AF: 0.296 AC: 622 AN: 2104

Alfa AF: 0.307 Hom.: 2613

Bravo AF: 0.283

Asia WGS AF: 0.278 AC: 967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.1
DANN	Benign	0.70
PhyloP100		0.14

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: rs1308020;

hg19: chr11-65497558;