rs1029718

Variant names:

• chr7-16004675-G-C
• rs1029718

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.164 AC: 6801 AN: 41474

American (AMR) AF: 0.450 AC: 6857 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 986 AN: 3468

East Asian (EAS) AF: 0.474 AC: 2438 AN: 5142

South Asian (SAS) AF: 0.536 AC: 2581 AN: 4818

European-Finnish (FIN) AF: 0.515 AC: 5432 AN: 10546

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27709 AN: 67934

Other (OTH) AF: 0.348 AC: 735 AN: 2112

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
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs1029718; hg19: chr7-16044300;