ENST00000827669.1:n.222+6641A>G

Variant names:

• chr13-37370791-A-G
• rs1324023
• ENST00000827669.1:n.222+6641A>G

Variant summary

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

The ENST00000827669.1(ENSG00000307651):​n.222+6641A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 151,964 control chromosomes in the GnomAD database, including 20,143 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 (20143 hom., cov: 32)
• Consequence: ENSG00000307651 ENST00000827669.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 0 publications found

Genes affected

ENSG00000307651 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903159	XR_007063761.1	n.243+6641A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307651	ENST00000827669.1	n.222+6641A>G		intron_variant	Intron 2 of 3
ENSG00000307651	ENST00000827670.1	n.273+6641A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77404 AN: 151846 Hom.: 20131 Cov.: 32

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.510 AC: 77460 AN: 151964 Hom.: 20143 Cov.: 32 AF XY: 0.517 AC XY: 38411 AN XY: 74298

African (AFR) AF: 0.541 AC: 22432 AN: 41426

American (AMR) AF: 0.541 AC: 8260 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1462 AN: 3468

East Asian (EAS) AF: 0.782 AC: 4023 AN: 5144

South Asian (SAS) AF: 0.538 AC: 2587 AN: 4810

European-Finnish (FIN) AF: 0.521 AC: 5511 AN: 10582

Middle Eastern (MID) AF: 0.449 AC: 131 AN: 292

European-Non Finnish (NFE) AF: 0.465 AC: 31605 AN: 67960

Other (OTH) AF: 0.494 AC: 1043 AN: 2110

Alfa AF: 0.478 Hom.: 9325

Bravo AF: 0.515

Asia WGS AF: 0.680 AC: 2361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.44
DANN	Benign	0.53
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1324023; hg19: chr13-37944928;