7-128410394-G-A

Position:

• chr7-128410394-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0178 in 152,804 control chromosomes in the GnomAD database, including 41 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 0.018 (41 hom., cov: 33)
  • Exomes 𝑓: 0.023 (0 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0178 (2713/152364) while in subpopulation SAS AF= 0.0547 (264/4828). AF 95% confidence interval is 0.0493. There are 41 homozygotes in gnomad4. There are 1333 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 41 gene

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: 0.0178 AC: 2715 AN: 152246 Hom.: 41 Cov.: 33

Gnomad AFR AF: 0.00610

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0196

Gnomad ASJ AF: 0.0193

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0550

Gnomad FIN AF: 0.00659

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0249

Gnomad OTH AF: 0.0206

GnomAD4 exome AF: 0.0227 AC: 10 AN: 440 Hom.: 0 AF XY: 0.0248 AC XY: 6 AN XY: 242

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0417

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0267

Gnomad4 OTH exome AF: 0.0263

GnomAD4 genome AF: 0.0178 AC: 2713 AN: 152364 Hom.: 41 Cov.: 33 AF XY: 0.0179 AC XY: 1333 AN XY: 74504

Gnomad4 AFR AF: 0.00608

Gnomad4 AMR AF: 0.0196

Gnomad4 ASJ AF: 0.0193

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0547

Gnomad4 FIN AF: 0.00659

Gnomad4 NFE AF: 0.0249

Gnomad4 OTH AF: 0.0203

Alfa AF: 0.0185 Hom.: 5

Bravo AF: 0.0170

Asia WGS AF: 0.0280 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.5
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72624931; hg19: chr7-128050448;