ENST00000779046.1:n.260+7349G>A

Variant names:

• chr1-38434971-G-A
• rs7530233
• ENST00000779046.1:n.260+7349G>A

Variant summary

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

The ENST00000779046.1(ENSG00000301471):​n.260+7349G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 152,032 control chromosomes in the GnomAD database, including 9,799 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 0.35 (9799 hom., cov: 33)
• Consequence: ENSG00000301471 ENST00000779046.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360
• Publications: 4 publications found

Genes affected

ENSG00000301471 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984943	XR_001737993.2	n.405+6232C>T		intron_variant	Intron 2 of 2
LOC105378657	XR_947210.3	n.424+65025C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301471	ENST00000779046.1	n.260+7349G>A		intron_variant	Intron 1 of 1
ENSG00000301471	ENST00000779047.1	n.260+7349G>A		intron_variant	Intron 1 of 2
ENSG00000301471	ENST00000779048.1	n.260+7349G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53270 AN: 151914 Hom.: 9799 Cov.: 33

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.350 AC: 53285 AN: 152032 Hom.: 9799 Cov.: 33 AF XY: 0.350 AC XY: 25969 AN XY: 74286

African (AFR) AF: 0.283 AC: 11720 AN: 41456

American (AMR) AF: 0.305 AC: 4658 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1661 AN: 3468

East Asian (EAS) AF: 0.121 AC: 624 AN: 5166

South Asian (SAS) AF: 0.322 AC: 1551 AN: 4818

European-Finnish (FIN) AF: 0.414 AC: 4378 AN: 10570

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.405 AC: 27537 AN: 67964

Other (OTH) AF: 0.369 AC: 779 AN: 2110

Alfa AF: 0.381 Hom.: 27893

Bravo AF: 0.337

Asia WGS AF: 0.268 AC: 935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.9
DANN	Benign	0.64
PhyloP100		0.036

Splicing

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

Other links and lift over

dbSNP: rs7530233; hg19: chr1-38900643;