7-16785037-G-A

Position:

• chr7-16785037-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.71 in 152,004 control chromosomes in the GnomAD database, including 38,454 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 0.71 (38454 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107820 AN: 151886 Hom.: 38439 Cov.: 32

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.796

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.710 AC: 107889 AN: 152004 Hom.: 38454 Cov.: 32 AF XY: 0.708 AC XY: 52609 AN XY: 74312

Gnomad4 AFR AF: 0.641

Gnomad4 AMR AF: 0.748

Gnomad4 ASJ AF: 0.808

Gnomad4 EAS AF: 0.717

Gnomad4 SAS AF: 0.739

Gnomad4 FIN AF: 0.627

Gnomad4 NFE AF: 0.746

Gnomad4 OTH AF: 0.731

Alfa AF: 0.745 Hom.: 69317

Bravo AF: 0.715

Asia WGS AF: 0.703 AC: 2444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.055
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1037791; hg19: chr7-16824662;