rs978739

chr7-122995846-T-Cchr7-122995846-T-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 0.359 in 489,260 control chromosomes in the GnomAD database, including 32,486 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 0.37 (10387 hom., cov: 32)
  • Exomes 𝑓: 0.36 (22099 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.592

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.44 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: 0.365 AC: 55431 AN: 151806 Hom.: 10376 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.350

GnomAD4 exome AF: 0.356 AC: 120240 AN: 337336 Hom.: 22099 AF XY: 0.360 AC XY: 62135 AN XY: 172522

Gnomad4 AFR exome AF: 0.416

Gnomad4 AMR exome AF: 0.287

Gnomad4 ASJ exome AF: 0.319

Gnomad4 EAS exome AF: 0.342

Gnomad4 SAS exome AF: 0.468

Gnomad4 FIN exome AF: 0.380

Gnomad4 NFE exome AF: 0.350

Gnomad4 OTH exome AF: 0.353

GnomAD4 genome AF: 0.365 AC: 55474 AN: 151924 Hom.: 10387 Cov.: 32 AF XY: 0.366 AC XY: 27147 AN XY: 74248

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.455

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.355

Alfa AF: 0.269 Hom.: 988

Bravo AF: 0.356

Asia WGS AF: 0.417 AC: 1449 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	5.1
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs978739; hg19: chr7-122635900;