rs1207731

Positions:

• chr7-97020044-A-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 0.183 in 152,092 control chromosomes in the GnomAD database, including 2,692 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 0.18 (2692 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.609

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.208 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: 0.183 AC: 27782 AN: 151974 Hom.: 2691 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.183 AC: 27798 AN: 152092 Hom.: 2692 Cov.: 32 AF XY: 0.177 AC XY: 13130 AN XY: 74334

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.179

Alfa AF: 0.204 Hom.: 6661

Bravo AF: 0.185

Asia WGS AF: 0.136 AC: 471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	14
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1207731; hg19: chr7-96649356;