9-1670196-G-C

Variant names:

• chr9-1670196-G-C
• rs4740635

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.251 in 152,052 control chromosomes in the GnomAD database, including 6,054 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 0.25 (6054 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.314

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.329 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

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38099 AN: 151934 Hom.: 6058 Cov.: 33

Gnomad AFR AF: 0.0748

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.251 AC: 38092 AN: 152052 Hom.: 6054 Cov.: 33 AF XY: 0.254 AC XY: 18839 AN XY: 74310

Gnomad4 AFR AF: 0.0746

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.291

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.259

Alfa AF: 0.185 Hom.: 449

Bravo AF: 0.231

Asia WGS AF: 0.165 AC: 575 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	16
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4740635; hg19: chr9-1670196; COSMIC: COSV69441339;