rs7004029

Variant names:

• chr8-144720652-T-C
• rs7004029
• ENST00000775706.1:n.306-9325T>C

Variant summary

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

The ENST00000775706.1(ENSG00000290885):​n.306-9325T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 152,140 control chromosomes in the GnomAD database, including 10,822 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 0.36 (10822 hom., cov: 33)
• Consequence: ENSG00000290885 ENST00000775706.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209
• Publications: 7 publications found

Genes affected

ENSG00000290885 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.562 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
ENSG00000290885	ENST00000775706.1	n.306-9325T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54780 AN: 152022 Hom.: 10827 Cov.: 33

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.360 AC: 54783 AN: 152140 Hom.: 10822 Cov.: 33 AF XY: 0.368 AC XY: 27340 AN XY: 74372

African (AFR) AF: 0.200 AC: 8291 AN: 41520

American (AMR) AF: 0.383 AC: 5852 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1297 AN: 3470

East Asian (EAS) AF: 0.465 AC: 2406 AN: 5170

South Asian (SAS) AF: 0.580 AC: 2795 AN: 4818

European-Finnish (FIN) AF: 0.488 AC: 5168 AN: 10584

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27836 AN: 67976

Other (OTH) AF: 0.368 AC: 777 AN: 2110

Alfa AF: 0.399 Hom.: 6756

Bravo AF: 0.340

Asia WGS AF: 0.541 AC: 1880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.6
DANN	Benign	0.40
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs7004029; hg19: chr8-145946037;