rs7805053

Variant names:

• chr7-9684086-C-A
• rs7805053
• ENST00000447999.2:n.272-23915C>A

Your query was ambiguous. Multiple possible variants found:

• chr7-9684086-C-A
• chr7-9684086-C-G
• chr7-9684086-C-T

Variant summary

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

The ENST00000447999.2(ENSG00000234710):​n.272-23915C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 151,926 control chromosomes in the GnomAD database, including 4,867 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 0.24 (4867 hom., cov: 32)
• Consequence: ENSG00000234710 ENST00000447999.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357
• Publications: 3 publications found

Genes affected

ENSG00000234710 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000447999.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105375148	NR_187872.1		n.239-32704C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000234710	ENST00000447999.2	TSL:3	n.272-23915C>A		intron	N/A
	ENSG00000234710	ENST00000657272.2		n.280-32704C>A		intron	N/A
	ENSG00000234710	ENST00000731126.1		n.242-23915C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36537 AN: 151808 Hom.: 4866 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.241 AC: 36551 AN: 151926 Hom.: 4867 Cov.: 32 AF XY: 0.240 AC XY: 17851 AN XY: 74248

African (AFR) AF: 0.131 AC: 5433 AN: 41488

American (AMR) AF: 0.206 AC: 3149 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1044 AN: 3462

East Asian (EAS) AF: 0.223 AC: 1144 AN: 5138

South Asian (SAS) AF: 0.304 AC: 1465 AN: 4822

European-Finnish (FIN) AF: 0.316 AC: 3336 AN: 10542

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20100 AN: 67888

Other (OTH) AF: 0.243 AC: 512 AN: 2110

Alfa AF: 0.351 Hom.: 28891

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.39
DANN	Benign	0.29
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs7805053; hg19: chr7-9723716;