rs7807771

Variant names:

• chr7-85519647-A-G
• rs7807771
• ENST00000795228.1:n.64-45220T>C

Variant summary

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

The ENST00000795228.1(ENSG00000303520):​n.64-45220T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 152,048 control chromosomes in the GnomAD database, including 7,314 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 (7314 hom., cov: 32)
• Consequence: ENSG00000303520 ENST00000795228.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270
• Publications: 9 publications found

Genes affected

ENSG00000303520 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.558 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
ENSG00000303520	ENST00000795228.1	n.64-45220T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33065 AN: 151930 Hom.: 7280 Cov.: 32

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.0720

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0385

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0670

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.218 AC: 33165 AN: 152048 Hom.: 7314 Cov.: 32 AF XY: 0.214 AC XY: 15892 AN XY: 74338

African (AFR) AF: 0.564 AC: 23341 AN: 41416

American (AMR) AF: 0.200 AC: 3048 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0720 AC: 250 AN: 3472

East Asian (EAS) AF: 0.105 AC: 544 AN: 5166

South Asian (SAS) AF: 0.118 AC: 571 AN: 4824

European-Finnish (FIN) AF: 0.0385 AC: 408 AN: 10610

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0669 AC: 4550 AN: 67974

Other (OTH) AF: 0.185 AC: 390 AN: 2104

Alfa AF: 0.112 Hom.: 6913

Bravo AF: 0.242

Asia WGS AF: 0.187 AC: 650 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.46
PhyloP100		0.027

Splicing

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

Other links and lift over

dbSNP: rs7807771; hg19: chr7-85148963; COSMIC: COSV63294259;