rs11765584

Variant names:

• chr7-64124406-G-A
• rs11765584
• ENST00000434932.1:n.115+3861G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-64124406-G-A
• chr7-64124406-G-C

Variant summary

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

The ENST00000434932.1(ENSG00000290564):​n.115+3861G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,076 control chromosomes in the GnomAD database, including 5,756 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 0.25 (5756 hom., cov: 32)
• Consequence: ENSG00000290564 ENST00000434932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.227
• Publications: 6 publications found

Genes affected

ENSG00000290564 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000434932.1. 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
	ENSG00000290564	ENST00000434932.1	TSL:1	n.115+3861G>A		intron	N/A
	ENSG00000290564	ENST00000715349.1		n.662+3861G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37887 AN: 151958 Hom.: 5753 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.00367

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.249 AC: 37900 AN: 152076 Hom.: 5756 Cov.: 32 AF XY: 0.251 AC XY: 18634 AN XY: 74332

African (AFR) AF: 0.102 AC: 4253 AN: 41494

American (AMR) AF: 0.275 AC: 4200 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1057 AN: 3464

East Asian (EAS) AF: 0.00368 AC: 19 AN: 5170

South Asian (SAS) AF: 0.226 AC: 1087 AN: 4816

European-Finnish (FIN) AF: 0.383 AC: 4048 AN: 10574

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.328 AC: 22302 AN: 67978

Other (OTH) AF: 0.230 AC: 484 AN: 2108

Alfa AF: 0.284 Hom.: 4782

Bravo AF: 0.234

Asia WGS AF: 0.107 AC: 370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.5
DANN	Benign	0.30
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs11765584; hg19: chr7-63584784;