chr7-16885894-A-G

Variant names:

• chr7-16885894-A-G
• rs10950639
• ENST00000766377.1:n.212-28062A>G

Variant summary

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

The ENST00000766377.1(ENSG00000289189):​n.212-28062A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,108 control chromosomes in the GnomAD database, including 3,750 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 0.22 (3750 hom., cov: 32)
• Consequence: ENSG00000289189 ENST00000766377.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160
• Publications: 3 publications found

Genes affected

ENSG00000289189 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.234 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
ENSG00000289189	ENST00000766377.1	n.212-28062A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33323 AN: 151988 Hom.: 3744 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.219 AC: 33345 AN: 152108 Hom.: 3750 Cov.: 32 AF XY: 0.221 AC XY: 16465 AN XY: 74370

African (AFR) AF: 0.238 AC: 9855 AN: 41492

American (AMR) AF: 0.237 AC: 3617 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 808 AN: 3468

East Asian (EAS) AF: 0.146 AC: 756 AN: 5180

South Asian (SAS) AF: 0.207 AC: 998 AN: 4814

European-Finnish (FIN) AF: 0.249 AC: 2634 AN: 10570

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.204 AC: 13867 AN: 67994

Other (OTH) AF: 0.262 AC: 553 AN: 2114

Alfa AF: 0.214 Hom.: 4567

Bravo AF: 0.220

Asia WGS AF: 0.214 AC: 742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.68
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs10950639; hg19: chr7-16925518;