rs7847869

Variant names:

• chr9-111973743-C-T
• rs7847869
• ENST00000765698.1:n.109+4247C>T

Variant summary

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

The ENST00000765698.1(ENSG00000299696):​n.109+4247C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,184 control chromosomes in the GnomAD database, including 1,454 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 0.13 (1454 hom., cov: 32)
• Consequence: ENSG00000299696 ENST00000765698.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213
• Publications: 1 publications found

Genes affected

ENSG00000299696 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.184 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
ENSG00000299696	ENST00000765698.1	n.109+4247C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20392 AN: 152066 Hom.: 1454 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.0512

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.134 AC: 20403 AN: 152184 Hom.: 1454 Cov.: 32 AF XY: 0.133 AC XY: 9912 AN XY: 74382

African (AFR) AF: 0.106 AC: 4411 AN: 41514

American (AMR) AF: 0.190 AC: 2896 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 537 AN: 3472

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5190

South Asian (SAS) AF: 0.0510 AC: 246 AN: 4824

European-Finnish (FIN) AF: 0.156 AC: 1653 AN: 10590

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10254 AN: 67994

Other (OTH) AF: 0.137 AC: 289 AN: 2116

Alfa AF: 0.141 Hom.: 195

Bravo AF: 0.134

Asia WGS AF: 0.0380 AC: 133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.54
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs7847869; hg19: chr9-114736023;