rs1029718

Variant names:

• chr7-16004675-G-C
• rs1029718

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;