rs7848992

Positions:

• chr9-15021050-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000609203.1(ENSG00000291185):​n.765-3992A>G variant causes a intron, non coding transcript 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: ENST00000609203.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000609203.1	n.765-3992A>G		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.0937

Gnomad4 AMR AF: 0.0348

Gnomad4 ASJ AF: 0.0314

Gnomad4 EAS AF: 0.0966

Gnomad4 SAS AF: 0.0214

Gnomad4 FIN AF: 0.0367

Gnomad4 NFE AF: 0.0112

Gnomad4 OTH AF: 0.0336

Alfa AF: 0.0217 Hom.: 25

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

Splicing

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

Publications

LitVar

Other links and lift over

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