rs1757948

chr9-78695764-A-Cchr9-78695764-A-G

Variant summary

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

The variant allele was found at a frequency of 0.262 in 151,818 control chromosomes in the GnomAD database, including 6,293 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 0.26 (6293 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.65

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.389 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

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39757 AN: 151698 Hom.: 6285 Cov.: 32

Gnomad AFR AF: 0.0846

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.262 AC: 39778 AN: 151818 Hom.: 6293 Cov.: 32 AF XY: 0.267 AC XY: 19831 AN XY: 74170

Gnomad4 AFR AF: 0.0844

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.289

Alfa AF: 0.294 Hom.: 8087

Bravo AF: 0.258

Asia WGS AF: 0.305 AC: 1059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	14
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1757948; hg19: chr9-81310680; COSMIC: COSV60363461;