rs7848992

Variant names:

• chr9-15021050-T-C
• rs7848992
• ENST00000609203.1:n.765-3992A>G

Variant summary

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

The ENST00000609203.1(ENSG00000291185):​n.765-3992A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0418 in 152,264 control chromosomes in the GnomAD database, including 257 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 0.042 (257 hom., cov: 32)
• Consequence: ENSG00000291185 ENST00000609203.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 0 publications found

Genes affected

ENSG00000291185 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0912 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
ENSG00000291185	ENST00000609203.1	n.765-3992A>G		intron_variant	Intron 4 of 9	2
ENSG00000291185	ENST00000759520.1	n.313-20641A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0418 AC: 6363 AN: 152144 Hom.: 256 Cov.: 32

Gnomad AFR AF: 0.0939

Gnomad AMI AF: 0.00220

Gnomad AMR AF: 0.0346

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.0970

Gnomad SAS AF: 0.0214

Gnomad FIN AF: 0.0367

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0112

Gnomad OTH AF: 0.0316

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

GnomAD4 genome AF: 0.0418 AC: 6372 AN: 152264 Hom.: 257 Cov.: 32 AF XY: 0.0410 AC XY: 3050 AN XY: 74436

African (AFR) AF: 0.0937 AC: 3893 AN: 41554

American (AMR) AF: 0.0348 AC: 532 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0314 AC: 109 AN: 3466

East Asian (EAS) AF: 0.0966 AC: 500 AN: 5176

South Asian (SAS) AF: 0.0214 AC: 103 AN: 4814

European-Finnish (FIN) AF: 0.0367 AC: 389 AN: 10604

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0112 AC: 762 AN: 68034

Other (OTH) AF: 0.0336 AC: 71 AN: 2114

Alfa AF: 0.0241 Hom.: 222

Bravo AF: 0.0445

Asia WGS AF: 0.0730 AC: 254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.097
DANN	Benign	0.64
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs7848992; hg19: chr9-15021048; COSMIC: COSV67745215;