rs11590421

Variant names:

• chr1-38528443-G-A
• rs11590421
• ENST00000766956.1:n.240+66G>A

Variant summary

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

The ENST00000766956.1(ENSG00000299856):​n.240+66G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,202 control chromosomes in the GnomAD database, including 1,893 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 0.15 (1893 hom., cov: 32)
• Consequence: ENSG00000299856 ENST00000766956.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.944
• Publications: 3 publications found

Genes affected

ENSG00000299856 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766956.1. 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
	ENSG00000299856	ENST00000766956.1		n.240+66G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22450 AN: 152084 Hom.: 1893 Cov.: 32

Gnomad AFR AF: 0.0905

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.0251

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.148 AC: 22450 AN: 152202 Hom.: 1893 Cov.: 32 AF XY: 0.147 AC XY: 10905 AN XY: 74406

African (AFR) AF: 0.0903 AC: 3750 AN: 41524

American (AMR) AF: 0.125 AC: 1914 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 684 AN: 3470

East Asian (EAS) AF: 0.0253 AC: 131 AN: 5174

South Asian (SAS) AF: 0.124 AC: 597 AN: 4820

European-Finnish (FIN) AF: 0.196 AC: 2079 AN: 10598

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12840 AN: 68006

Other (OTH) AF: 0.158 AC: 334 AN: 2112

Alfa AF: 0.177 Hom.: 8269

Bravo AF: 0.141

Asia WGS AF: 0.0640 AC: 223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.21
DANN	Benign	0.22
PhyloP100		-0.94

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: rs11590421;

hg19: chr1-38994115;