rs7865955

Variant names:

• chr9-6408247-G-C
• rs7865955
• ENST00000783087.1:n.*87C>G

Variant summary

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

The ENST00000783087.1(ENSG00000301961):​n.*87C>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 152,076 control chromosomes in the GnomAD database, including 21,000 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 0.51 (21000 hom., cov: 33)
• Consequence: ENSG00000301961 ENST00000783087.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.979
• Publications: 5 publications found

Genes affected

ENSG00000301961 (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 (EAS) allele frequency at 95% confidence interval = 0.704 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
ENSG00000301961	ENST00000783087.1	n.*87C>G		downstream_gene_variant
ENSG00000301961	ENST00000783088.1	n.*87C>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77946 AN: 151958 Hom.: 20984 Cov.: 33

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.513 AC: 77978 AN: 152076 Hom.: 21000 Cov.: 33 AF XY: 0.514 AC XY: 38189 AN XY: 74344

African (AFR) AF: 0.350 AC: 14505 AN: 41440

American (AMR) AF: 0.541 AC: 8278 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1940 AN: 3468

East Asian (EAS) AF: 0.723 AC: 3747 AN: 5180

South Asian (SAS) AF: 0.632 AC: 3052 AN: 4830

European-Finnish (FIN) AF: 0.563 AC: 5941 AN: 10560

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.571 AC: 38801 AN: 67994

Other (OTH) AF: 0.513 AC: 1085 AN: 2114

Alfa AF: 0.545 Hom.: 2938

Bravo AF: 0.504

Asia WGS AF: 0.699 AC: 2429 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	7.2
DANN	Benign	0.83
PhyloP100		0.98

Splicing

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

Other links and lift over

dbSNP: rs7865955; hg19: chr9-6408247; COSMIC: COSV71883187;