rs7950390

chr11-4610122-T-G

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 0.16 in 152,088 control chromosomes in the GnomAD database, including 4,040 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 0.16 (4040 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.42 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: 0.160 AC: 24273 AN: 151970 Hom.: 4025 Cov.: 32

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0993

Gnomad ASJ AF: 0.0401

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0230

Gnomad FIN AF: 0.0186

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0647

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.160 AC: 24323 AN: 152088 Hom.: 4040 Cov.: 32 AF XY: 0.153 AC XY: 11398 AN XY: 74360

Gnomad4 AFR AF: 0.426

Gnomad4 AMR AF: 0.0993

Gnomad4 ASJ AF: 0.0401

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0226

Gnomad4 FIN AF: 0.0186

Gnomad4 NFE AF: 0.0648

Gnomad4 OTH AF: 0.142

Alfa AF: 0.0782 Hom.: 1098

Bravo AF: 0.176

Asia WGS AF: 0.0410 AC: 142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	3.2
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7950390; hg19: chr11-4631352;