7-108908603-A-G

Variant names:

• chr7-108908603-A-G
• rs848353

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 0.136 in 152,092 control chromosomes in the GnomAD database, including 2,452 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 0.14 (2452 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20702 AN: 151974 Hom.: 2434 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.0747

Gnomad AMR AF: 0.0843

Gnomad ASJ AF: 0.0591

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.0734

Gnomad FIN AF: 0.0475

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0610

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.136 AC: 20760 AN: 152092 Hom.: 2452 Cov.: 32 AF XY: 0.134 AC XY: 9953 AN XY: 74362

African (AFR) AF: 0.318 AC: 13198 AN: 41470

American (AMR) AF: 0.0843 AC: 1286 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0591 AC: 205 AN: 3470

East Asian (EAS) AF: 0.142 AC: 732 AN: 5164

South Asian (SAS) AF: 0.0737 AC: 356 AN: 4832

European-Finnish (FIN) AF: 0.0475 AC: 504 AN: 10620

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0609 AC: 4141 AN: 67966

Other (OTH) AF: 0.122 AC: 256 AN: 2106

Alfa AF: 0.0856 Hom.: 3056

Bravo AF: 0.148

Asia WGS AF: 0.128 AC: 445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.7
DANN	Benign	0.75
PhyloP100		0.071

Splicing

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

Other links and lift over

dbSNP: rs848353; hg19: chr7-108548660;