rs1993894

Positions:

• chr7-64357110-G-A

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 0.339 in 151,678 control chromosomes in the GnomAD database, including 9,273 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 0.34 (9273 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.47 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: 0.338 AC: 51284 AN: 151560 Hom.: 9260 Cov.: 30

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.339 AC: 51347 AN: 151678 Hom.: 9273 Cov.: 30 AF XY: 0.336 AC XY: 24903 AN XY: 74126

Gnomad4 AFR AF: 0.476

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.291

Gnomad4 EAS AF: 0.353

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.354

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.317

Alfa AF: 0.315 Hom.: 972

Bravo AF: 0.344

Asia WGS AF: 0.314 AC: 1089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.7
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1993894; hg19: chr7-63817488;