rs1000620

Variant names:

• chr11-72798668-G-A
• rs1000620
• ENST00000624670.2:n.646-4391C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-72798668-G-A
• chr11-72798668-G-T

Variant summary

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

The ENST00000719213.1(ENSG00000293817):​n.265+4652G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 151,848 control chromosomes in the GnomAD database, including 20,141 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 0.51 (20141 hom., cov: 30)
• Consequence: ENSG00000293817 ENST00000719213.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0340
• Publications: 13 publications found

Genes affected

ENSG00000285693 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000719213.1. 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
	ENSG00000285693	ENST00000624670.2	TSL:6	n.646-4391C>T		intron	N/A
	ENSG00000293817	ENST00000719213.1		n.265+4652G>A		intron	N/A
	ENSG00000293817	ENST00000719214.1		n.259+4652G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77819 AN: 151730 Hom.: 20139 Cov.: 30

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.513 AC: 77855 AN: 151848 Hom.: 20141 Cov.: 30 AF XY: 0.513 AC XY: 38052 AN XY: 74190

African (AFR) AF: 0.532 AC: 22015 AN: 41392

American (AMR) AF: 0.554 AC: 8441 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2052 AN: 3468

East Asian (EAS) AF: 0.620 AC: 3193 AN: 5152

South Asian (SAS) AF: 0.552 AC: 2651 AN: 4804

European-Finnish (FIN) AF: 0.441 AC: 4652 AN: 10542

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33323 AN: 67926

Other (OTH) AF: 0.524 AC: 1107 AN: 2112

Alfa AF: 0.504 Hom.: 65844

Bravo AF: 0.521

Asia WGS AF: 0.554 AC: 1928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.1
DANN	Benign	0.59
PhyloP100		0.034

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: rs1000620;

hg19: chr11-72509713;