rs7730843

Variant names:

• chr5-36542210-G-A
• rs7730843
• ENST00000751409.1:n.110+10947C>T

Variant summary

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

The ENST00000751409.1(ENSG00000297854):​n.110+10947C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,092 control chromosomes in the GnomAD database, including 8,310 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 0.28 (8310 hom., cov: 32)
• Consequence: ENSG00000297854 ENST00000751409.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246
• Publications: 2 publications found

Genes affected

ENSG00000297854 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.553 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
ENSG00000297854	ENST00000751409.1	n.110+10947C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42981 AN: 151974 Hom.: 8273 Cov.: 32

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.0648

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.0687

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.283 AC: 43082 AN: 152092 Hom.: 8310 Cov.: 32 AF XY: 0.282 AC XY: 20961 AN XY: 74346

African (AFR) AF: 0.559 AC: 23170 AN: 41474

American (AMR) AF: 0.203 AC: 3102 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 550 AN: 3468

East Asian (EAS) AF: 0.0687 AC: 356 AN: 5182

South Asian (SAS) AF: 0.167 AC: 808 AN: 4826

European-Finnish (FIN) AF: 0.220 AC: 2318 AN: 10556

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12146 AN: 67990

Other (OTH) AF: 0.245 AC: 516 AN: 2106

Alfa AF: 0.204 Hom.: 2831

Bravo AF: 0.292

Asia WGS AF: 0.155 AC: 539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.87
DANN	Benign	0.17
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs7730843; hg19: chr5-36542312;