rs7805803

Variant names:

• chr7-50185795-G-A
• rs7805803
• ENST00000774254.1:n.255+11619C>T

Variant summary

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

The ENST00000774254.1(ENSG00000300822):​n.255+11619C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 152,014 control chromosomes in the GnomAD database, including 13,055 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 0.41 (13055 hom., cov: 32)
• Consequence: ENSG00000300822 ENST00000774254.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238
• Publications: 16 publications found

Genes affected

ENSG00000300822 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.462 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
ENSG00000300822	ENST00000774254.1	n.255+11619C>T		intron_variant	Intron 1 of 3
ENSG00000300822	ENST00000774255.1	n.171+11619C>T		intron_variant	Intron 1 of 3
ENSG00000300822	ENST00000774256.1	n.181+11619C>T		intron_variant	Intron 1 of 3
ENSG00000300822	ENST00000774257.1	n.253+11619C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61854 AN: 151896 Hom.: 13051 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.407 AC: 61868 AN: 152014 Hom.: 13055 Cov.: 32 AF XY: 0.400 AC XY: 29696 AN XY: 74302

African (AFR) AF: 0.348 AC: 14439 AN: 41448

American (AMR) AF: 0.447 AC: 6837 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1588 AN: 3470

East Asian (EAS) AF: 0.188 AC: 969 AN: 5166

South Asian (SAS) AF: 0.195 AC: 937 AN: 4816

European-Finnish (FIN) AF: 0.380 AC: 4012 AN: 10550

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.466 AC: 31663 AN: 67954

Other (OTH) AF: 0.401 AC: 849 AN: 2116

Alfa AF: 0.438 Hom.: 50438

Bravo AF: 0.410

Asia WGS AF: 0.191 AC: 662 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.2
DANN	Benign	0.66
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs7805803; hg19: chr7-50225391; COSMIC: COSV107154845;