rs806187

Variant names:

• chr7-127629585-T-C
• rs806187
• ENST00000787994.1:n.760+7751T>C

Variant summary

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

The ENST00000787994.1(ENSG00000302590):​n.760+7751T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 152,030 control chromosomes in the GnomAD database, including 14,539 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 0.40 (14539 hom., cov: 32)
• Consequence: ENSG00000302590 ENST00000787994.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 3 publications found

Genes affected

ENSG00000302590 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 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
ENSG00000302590	ENST00000787994.1	n.760+7751T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.395 AC: 60045 AN: 151912 Hom.: 14503 Cov.: 32

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.395 AC: 60120 AN: 152030 Hom.: 14539 Cov.: 32 AF XY: 0.394 AC XY: 29243 AN XY: 74298

African (AFR) AF: 0.691 AC: 28636 AN: 41432

American (AMR) AF: 0.299 AC: 4571 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1057 AN: 3472

East Asian (EAS) AF: 0.221 AC: 1141 AN: 5156

South Asian (SAS) AF: 0.371 AC: 1793 AN: 4828

European-Finnish (FIN) AF: 0.329 AC: 3477 AN: 10558

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18412 AN: 67982

Other (OTH) AF: 0.352 AC: 744 AN: 2112

Alfa AF: 0.338 Hom.: 1290

Bravo AF: 0.402

Asia WGS AF: 0.303 AC: 1055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.81
DANN	Benign	0.22
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs806187; hg19: chr7-127269639;