rs9379780

Variant names:

• chr6-25706943-G-A
• rs9379780
• ENST00000703602.1:c.703-11825G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-25706943-G-A
• chr6-25706943-G-C

Variant summary

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

The ENST00000703602.1(ENSG00000290217):​c.703-11825G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 152,026 control chromosomes in the GnomAD database, including 29,129 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 0.61 (29129 hom., cov: 32)
• Consequence: ENSG00000290217 ENST00000703602.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.96

Genes affected

ENSG00000290217 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290217	ENST00000703602.1	c.703-11825G>A		intron_variant	Intron 10 of 11			ENSP00000515390.1

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93388 AN: 151908 Hom.: 29081 Cov.: 32

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.615 AC: 93485 AN: 152026 Hom.: 29129 Cov.: 32 AF XY: 0.619 AC XY: 46037 AN XY: 74314

Gnomad4 AFR AF: 0.563

Gnomad4 AMR AF: 0.658

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.865

Gnomad4 SAS AF: 0.648

Gnomad4 FIN AF: 0.667

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.598

Alfa AF: 0.602 Hom.: 38700

Bravo AF: 0.612

Asia WGS AF: 0.749 AC: 2601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.11
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9379780; hg19: chr6-25707171;