rs1207739

Positions:

• chr7-97030880-G-A
• chr7-97030880-G-T

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 0.0574 in 152,282 control chromosomes in the GnomAD database, including 328 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 0.057 (328 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.543

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.97030880G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0574 AC: 8738 AN: 152164 Hom.: 328 Cov.: 33

Gnomad AFR AF: 0.0143

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.0526

Gnomad ASJ AF: 0.0625

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0872

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0776

Gnomad OTH AF: 0.0584

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

GnomAD4 genome AF: 0.0574 AC: 8738 AN: 152282 Hom.: 328 Cov.: 33 AF XY: 0.0583 AC XY: 4342 AN XY: 74454

Gnomad4 AFR AF: 0.0142

Gnomad4 AMR AF: 0.0525

Gnomad4 ASJ AF: 0.0625

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0875

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.0776

Gnomad4 OTH AF: 0.0578

Alfa AF: 0.0711 Hom.: 634

Bravo AF: 0.0507

Asia WGS AF: 0.0330 AC: 116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.87
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1207739; hg19: chr7-96660192;