rs7756290

Variant names:

• chr6-31102539-A-T
• rs7756290

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;