rs1029718

chr7-16004675-G-C

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 0.355 in 151,946 control chromosomes in the GnomAD database, including 10,939 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 0.35 (10939 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.929

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.518 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: 0.355 AC: 53912 AN: 151826 Hom.: 10929 Cov.: 31

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.355 AC: 53939 AN: 151946 Hom.: 10939 Cov.: 31 AF XY: 0.364 AC XY: 26998 AN XY: 74256

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.474

Gnomad4 SAS AF: 0.536

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.348

Alfa AF: 0.377 Hom.: 1464

Bravo AF: 0.339

Asia WGS AF: 0.490 AC: 1704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
Cadd	Benign	19
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1029718; hg19: chr7-16044300;