chr6-7725824-A-G

Variant names:

• chr6-7725824-A-G
• rs1107495

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.207 in 152,262 control chromosomes in the GnomAD database, including 3,677 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 0.21 (3677 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31534 AN: 152144 Hom.: 3673 Cov.: 33

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.207 AC: 31554 AN: 152262 Hom.: 3677 Cov.: 33 AF XY: 0.215 AC XY: 16018 AN XY: 74456

African (AFR) AF: 0.170 AC: 7070 AN: 41564

American (AMR) AF: 0.333 AC: 5101 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 417 AN: 3472

East Asian (EAS) AF: 0.436 AC: 2255 AN: 5172

South Asian (SAS) AF: 0.223 AC: 1074 AN: 4826

European-Finnish (FIN) AF: 0.262 AC: 2783 AN: 10608

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12312 AN: 67998

Other (OTH) AF: 0.198 AC: 419 AN: 2116

Alfa AF: 0.189 Hom.: 9453

Bravo AF: 0.210

Asia WGS AF: 0.369 AC: 1281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.5
DANN	Benign	0.49
PhyloP100		0.0060
PromoterAI		-0.0088	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1107495; hg19: chr6-7726057;