rs11765584

chr7-64124406-G-Achr7-64124406-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000434932.1(ENSG00000290564):n.115+3861G>A variant causes a intron, non coding transcript 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: ENST00000434932.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.227

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000434932.1	n.115+3861G>A		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.00368

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.230

Alfa AF: 0.293 Hom.: 3411

Bravo AF: 0.234

Asia WGS AF: 0.107 AC: 370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	4.5
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11765584; hg19: chr7-63584784;