chr6-25706943-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

Genes affected

ENSG00000290217 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.563 AC: 23310 AN: 41436

American (AMR) AF: 0.658 AC: 10063 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1855 AN: 3470

East Asian (EAS) AF: 0.865 AC: 4480 AN: 5182

South Asian (SAS) AF: 0.648 AC: 3114 AN: 4808

European-Finnish (FIN) AF: 0.667 AC: 7046 AN: 10568

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.611 AC: 41544 AN: 67964

Other (OTH) AF: 0.598 AC: 1258 AN: 2102

Alfa AF: 0.610 Hom.: 97340

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
PhyloP100		-4.0

Splicing

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

Other links and lift over

dbSNP: rs9379780; hg19: chr6-25707171;