chr7-138314909-A-G

Position:

• chr7-138314909-A-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 0.172 in 152,062 control chromosomes in the GnomAD database, including 2,709 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 0.17 (2709 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.355 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: 0.172 AC: 26154 AN: 151946 Hom.: 2712 Cov.: 32

Gnomad AFR AF: 0.0731

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.172 AC: 26142 AN: 152062 Hom.: 2709 Cov.: 32 AF XY: 0.175 AC XY: 13008 AN XY: 74322

Gnomad4 AFR AF: 0.0730

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.183

Alfa AF: 0.178 Hom.: 318

Bravo AF: 0.165

Asia WGS AF: 0.289 AC: 1003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.1
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs392162; hg19: chr7-137999654;