rs7068215

Variant names:

• chr10-100100113-A-G
• rs7068215
• ENST00000807894.1:n.430+3876A>G

Variant summary

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

The ENST00000807894.1(ENSG00000305032):​n.430+3876A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 151,618 control chromosomes in the GnomAD database, including 9,413 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 (9413 hom., cov: 32)
• Consequence: ENSG00000305032 ENST00000807894.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 8 publications found

Genes affected

ENSG00000305032 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.389 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
ENSG00000305032	ENST00000807894.1	n.430+3876A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52387 AN: 151498 Hom.: 9397 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.0684

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.346 AC: 52448 AN: 151618 Hom.: 9413 Cov.: 32 AF XY: 0.339 AC XY: 25091 AN XY: 74054

African (AFR) AF: 0.319 AC: 13123 AN: 41188

American (AMR) AF: 0.383 AC: 5835 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1060 AN: 3472

East Asian (EAS) AF: 0.0680 AC: 351 AN: 5162

South Asian (SAS) AF: 0.212 AC: 1017 AN: 4806

European-Finnish (FIN) AF: 0.299 AC: 3145 AN: 10516

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.393 AC: 26695 AN: 67912

Other (OTH) AF: 0.372 AC: 787 AN: 2114

Alfa AF: 0.361 Hom.: 1379

Bravo AF: 0.352

Asia WGS AF: 0.186 AC: 649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.66
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7068215; hg19: chr10-101859870;