rs7694828

Variant names:

• chr4-74320687-A-C
• rs7694828
• ENST00000805841.1:n.298+9511T>G

Your query was ambiguous. Multiple possible variants found:

• chr4-74320687-A-C
• chr4-74320687-A-G
• chr4-74320687-A-T

Variant summary

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

The ENST00000805841.1(ENSG00000304732):​n.298+9511T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0591 in 152,220 control chromosomes in the GnomAD database, including 599 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 0.059 (599 hom., cov: 32)
• Consequence: ENSG00000304732 ENST00000805841.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.610
• Publications: 3 publications found

Genes affected

ENSG00000304732 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377276	NR_188415.1	n.298+9511T>G		intron_variant	Intron 2 of 2
LOC105377276	NR_188416.1	n.272+9511T>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304732	ENST00000805841.1	n.298+9511T>G		intron_variant	Intron 2 of 2
ENSG00000304732	ENST00000805842.1	n.395+9511T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0589 AC: 8960 AN: 152102 Hom.: 596 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0504

Gnomad ASJ AF: 0.00375

Gnomad EAS AF: 0.0523

Gnomad SAS AF: 0.0764

Gnomad FIN AF: 0.00895

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0122

Gnomad OTH AF: 0.0593

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

GnomAD4 genome AF: 0.0591 AC: 9000 AN: 152220 Hom.: 599 Cov.: 32 AF XY: 0.0593 AC XY: 4410 AN XY: 74426

African (AFR) AF: 0.157 AC: 6505 AN: 41512

American (AMR) AF: 0.0508 AC: 777 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00375 AC: 13 AN: 3468

East Asian (EAS) AF: 0.0526 AC: 273 AN: 5186

South Asian (SAS) AF: 0.0771 AC: 371 AN: 4812

European-Finnish (FIN) AF: 0.00895 AC: 95 AN: 10616

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0122 AC: 828 AN: 68016

Other (OTH) AF: 0.0597 AC: 126 AN: 2112

Alfa AF: 0.0259 Hom.: 39

Bravo AF: 0.0659

Asia WGS AF: 0.0890 AC: 310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.6
DANN	Benign	0.61
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs7694828; hg19: chr4-75186404;