rs989613

chr7-113806501-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 0.194 in 151,662 control chromosomes in the GnomAD database, including 3,168 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 0.19 (3168 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.318 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: 0.194 AC: 29451 AN: 151552 Hom.: 3153 Cov.: 31

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.194 AC: 29492 AN: 151662 Hom.: 3168 Cov.: 31 AF XY: 0.195 AC XY: 14451 AN XY: 74090

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.261

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.182

Alfa AF: 0.186 Hom.: 1306

Bravo AF: 0.207

Asia WGS AF: 0.301 AC: 1046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	9.6
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs989613; hg19: chr7-113446556;