rs7756290

chr6-31102539-A-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 0.151 in 152,092 control chromosomes in the GnomAD database, including 2,083 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 0.15 (2083 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.251 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: 0.151 AC: 22898 AN: 151974 Hom.: 2078 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.0970

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0989

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.151 AC: 22920 AN: 152092 Hom.: 2083 Cov.: 32 AF XY: 0.151 AC XY: 11213 AN XY: 74362

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.0967

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.0989

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.153

Alfa AF: 0.129 Hom.: 219

Bravo AF: 0.157

Asia WGS AF: 0.148 AC: 514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	2.6
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7756290; hg19: chr6-31070316;