rs1107664

chr18-61064481-G-Achr18-61064481-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.00652 in 152,210 control chromosomes in the GnomAD database, including 14 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 0.0065 (14 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.938

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00652 (993/152210) while in subpopulation SAS AF= 0.0504 (243/4822). AF 95% confidence interval is 0.0452. There are 14 homozygotes in gnomad4. There are 590 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 10 gene

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: 0.00641 AC: 975 AN: 152092 Hom.: 10 Cov.: 33

Gnomad AFR AF: 0.00657

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00341

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.0449

Gnomad SAS AF: 0.0501

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00162

Gnomad OTH AF: 0.00956

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

GnomAD4 genome AF: 0.00652 AC: 993 AN: 152210 Hom.: 14 Cov.: 33 AF XY: 0.00793 AC XY: 590 AN XY: 74432

Gnomad4 AFR AF: 0.00686

Gnomad4 AMR AF: 0.00340

Gnomad4 ASJ AF: 0.0121

Gnomad4 EAS AF: 0.0450

Gnomad4 SAS AF: 0.0504

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00162

Gnomad4 OTH AF: 0.0118

Alfa AF: 0.000576 Hom.: 0

Bravo AF: 0.00631

Asia WGS AF: 0.0420 AC: 144 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	9.8
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1107664; hg19: chr18-58731714; COSMIC: COSV50114980;